https://alida.informatik.uni-halle.de/api.php?action=feedcontributions&feedformat=atom&user=MoellerAlida - User contributions [en]2026-04-09T13:36:38ZUser contributionsMediaWiki 1.38.2https://alida.informatik.uni-halle.de/index.php?title=Tools&diff=355Tools2021-12-22T10:33:58Z<p>Moeller: </p>
<hr />
<div>__TOC__<br />
<br />
The Alida concept allows to generically run operators from command line or via GUI. In addition, it features Grappa, a visual workflow editor.<br />
<br />
== Graphical Operator Runner ==<br />
* support for saving/loading operator configuration parameters in XML format<br />
* handy configuration and control windows for configuring and running operators in graphical environments<br />
* batch mode option in GUIs to apply operators to sets of input data objects<br/><br/><br />
<br />
[[File:OpRunnerScreenshot.png|center]]<br />
<br />
== Commandline Operator Runner ==<br />
* flexible command line parser supporting regular expressions and various I/O channels (file, console)<br />
<br />
== Grappa - The Graphical Workflow Editor ==<br />
Grappa is a graphical workflow editor implemented based on the JGraphX library for visual graph editing. Grappa provides a workbench where multiple analysis workflows can be designed in parallel. Operators can be added as nodes to a workflow and edges be drawn between their parameter ports. The user gets immediate visual feedback if an edge is added between incompatible ports and no converter for automatic datatype conversion is available, and about the status of operator nodes, e.g., if they are unconfigured, ready to run or have already been executed. Workflows can be executed as a whole or in parts whereas Grappa takes care of recursively executing nodes that provide required input data for nodes to be executed, relying on functionality for topological sorting of nodes in a graph implemented in Alida's workflow class.<br />
<br />
[[File:GrappaScreenshot.png|center]]</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Tools&diff=354Tools2021-12-22T10:32:23Z<p>Moeller: </p>
<hr />
<div>The Alida concept allows to generically run operators from command line or via GUI. In addition, it features Grappa, a visual workflow editor.<br />
<br />
'''Graphical Operator Runner'''<br><br />
* support for saving/loading operator configuration parameters in XML format<br />
* handy configuration and control windows for configuring and running operators in graphical environments<br />
* batch mode option in GUIs to apply operators to sets of input data objects<br/><br/><br />
<br />
[[File:OpRunnerScreenshot.png|center]]<br />
<br />
'''Commandline Operator Runner'''<br><br />
* flexible command line parser supporting regular expressions and various I/O channels (file, console)<br />
<br />
'''Grappa - The Graphical Workflow Editor'''<br><br />
Grappa is a graphical workflow editor implemented based on the JGraphX library for visual graph editing. Grappa provides a workbench where multiple analysis workflows can be designed in parallel. Operators can be added as nodes to a workflow and edges be drawn between their parameter ports. The user gets immediate visual feedback if an edge is added between incompatible ports and no converter for automatic datatype conversion is available, and about the status of operator nodes, e.g., if they are unconfigured, ready to run or have already been executed. Workflows can be executed as a whole or in parts whereas Grappa takes care of recursively executing nodes that provide required input data for nodes to be executed, relying on functionality for topological sorting of nodes in a graph implemented in Alida's workflow class.<br />
<br />
[[File:GrappaScreenshot.png|center]]</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=353Main Page2021-12-22T10:31:23Z<p>Moeller: </p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top; width:65%;"" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
<!--<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
--><br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows. [[Tools|Learn More...]]<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top;width:35%;" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 3.0.2 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 04/2021: Alida 3.0.2 has been released coming with a more fancy handling of parameters on command line resulting in full support for dynamic operator interfaces from command line.<br />
* 05/2020: Alida 3.0 has been released!<br> The main novelty is a change in the online help system which was formerly based on the [https://de.wikipedia.org/wiki/JavaHelp_System Java Help System] and now relies on operator class annotations.<br />
* 07/2019: Alida 2.7.11 has been released.<br />
* 02/2019: Alida 2.7.10 has been released.<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Gnu PGP Public Key'''<br><br />
Since version 2.7.4 Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Tools&diff=352Tools2021-12-22T10:27:23Z<p>Moeller: </p>
<hr />
<div>__NOTOC__<br />
The Alida concept allows to generically run operators from command line or via GUI. In addition, it features Grappa, a visual workflow editor.<br />
<br />
'''Graphical Operator Runner'''<br><br />
* support for saving/loading operator configuration parameters in XML format<br />
* handy configuration and control windows for configuring and running operators in graphical environments<br />
* batch mode option in GUIs to apply operators to sets of input data objects<br/><br/><br />
<br />
[[File:OpRunnerScreenshot.png|center]]<br />
<br />
'''Commandline Operator Runner'''<br><br />
* flexible command line parser supporting regular expressions and various I/O channels (file, console)<br />
<br />
'''Grappa - The Graphical Workflow Editor'''<br><br />
Grappa is a graphical workflow editor implemented based on the JGraphX library for visual graph editing. Grappa provides a workbench where multiple analysis workflows can be designed in parallel. Operators can be added as nodes to a workflow and edges be drawn between their parameter ports. The user gets immediate visual feedback if an edge is added between incompatible ports and no converter for automatic datatype conversion is available, and about the status of operator nodes, e.g., if they are unconfigured, ready to run or have already been executed. Workflows can be executed as a whole or in parts whereas Grappa takes care of recursively executing nodes that provide required input data for nodes to be executed, relying on functionality for topological sorting of nodes in a graph implemented in Alida's workflow class.<br />
<br />
[[File:GrappaScreenshot.png|center]]</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Tools&diff=351Tools2021-12-22T10:25:32Z<p>Moeller: </p>
<hr />
<div>__NOTOC__<br />
The Alida concept allows to generically run operators from command line or via GUI. In addition, it features Grappa, a visual workflow editor.<br />
<br />
'''Graphical Operator Runner'''<br><br />
* support for saving/loading operator configuration parameters in XML format<br />
* handy configuration and control windows for configuring and running operators in graphical environments<br />
* batch mode option in GUIs to apply operators to sets of input data objects<br/><br/><br />
<br />
'''Commandline Operator Runner'''<br><br />
* flexible command line parser supporting regular expressions and various I/O channels (file, console)<br />
<br />
'''Grappa - The Graphical Workflow Editor'''<br><br />
Grappa is a graphical workflow editor implemented based on the JGraphX library for visual graph editing. Grappa provides a workbench where multiple analysis workflows can be designed in parallel. Operators can be added as nodes to a workflow and edges be drawn between their parameter ports. The user gets immediate visual feedback if an edge is added between incompatible ports and no converter for automatic datatype conversion is available, and about the status of operator nodes, e.g., if they are unconfigured, ready to run or have already been executed. Workflows can be executed as a whole or in parts whereas Grappa takes care of recursively executing nodes that provide required input data for nodes to be executed, relying on functionality for topological sorting of nodes in a graph implemented in Alida's workflow class.<br />
<br />
[[File:GrappaScreenshot.png|center]]</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Tools&diff=350Tools2021-12-22T10:13:12Z<p>Moeller: </p>
<hr />
<div>__NOTOC__<br />
The Alida concept allows to generically run operators from command line or via GUI. In addition, it features Grappa, a visual workflow editor.<br />
<br />
'''Graphical Operator Runner'''<br><br />
* support for saving/loading operator configuration parameters in XML format<br />
* handy configuration and control windows for configuring and running operators in graphical environments<br />
* batch mode option in GUIs to apply operators to sets of input data objects<br/><br/><br />
<br />
'''Commandline Operator Runner'''<br><br />
* flexible command line parser supporting regular expressions and various I/O channels (file, console)<br />
<br />
'''Grappa - The Graphical Workflow Editor'''<br><br />
Grappa is a graphical workflow editor implemented based on the JGraphX library for visual graph editing. Grappa provides a workbench where multiple analysis workflows can be designed in parallel. Operators can be added as nodes to a workflow and edges be drawn between their parameter ports. The user gets immediate visual feedback if an edge is added between incompatible ports and no converter for automatic datatype conversion is available, and about the status of operator nodes, e.g., if they are unconfigured, ready to run or have already been executed. Workflows can be executed as a whole or in parts whereas Grappa takes care of recursively executing nodes that provide required input data for nodes to be executed, relying on functionality for topological sorting of nodes in a graph implemented in Alida's workflow class.</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Tools&diff=349Tools2021-12-22T10:06:46Z<p>Moeller: Created page with "__NOTOC__ The Alida concept allows to generically run operators from command line or via GUI. In addition, it features Grappa, a visual workflow editor."</p>
<hr />
<div>__NOTOC__<br />
The Alida concept allows to generically run operators from command line or via GUI. In addition, it features Grappa, a visual workflow editor.</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=MediaWiki:Sidebar&diff=348MediaWiki:Sidebar2021-12-22T10:05:24Z<p>Moeller: Added page for runners and Grappa</p>
<hr />
<div>* navigation<br />
** mainpage|mainpage-description<br />
** features|Features<br />
** Screenshots|Screenshots<br />
** Downloads|Downloads<br />
** Installation|Installation<br />
** Support|Support<br />
** Quickstart|Quickstart and Code Examples<br />
** Tools|Operator Runners and Grappa<br />
** Projects|Related Projects and Publications<br />
** Acknowledge|Acknowledgements<br />
** Alida:About|Imprint<br />
* documentation<br />
** http://alida.informatik.uni-halle.de/downloads/manual/AlidaManual.pdf|Manual<br />
** http://alida.informatik.uni-halle.de/api/java/index.html|Javadoc API<br />
** frequently_asked_questions|FAQs<br />
* development<br />
** https://github.com/alida-hub/alida|Code on Github<br />
** https://github.com/alida-hub/alida/issues|Issue tracking<br />
* SEARCH<br />
* TOOLBOX<br />
* LANGUAGES</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=347Downloads2021-04-09T08:59:28Z<p>Moeller: </p>
<hr />
<div>==== Current Java release ====<br />
<br />
The current release of Alida is 3.0.2.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archival of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://doi.org/10.5281/zenodo.3855411 Alida 3.0], [[Image:zenodo.3855411.svg.png|165px|link=https://doi.org/10.5281/zenodo.3855411]]<br><br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.47586]]<br><br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 3.0.2 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (April 2021)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 3.0<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-javadoc.jar jar]<br />
| May 15th, 2020 <br />
|-<br />
| 2.7.13<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-javadoc.jar jar]<br />
| February 20th, 2020 <br />
|-<br />
| 2.7.12<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-javadoc.jar jar]<br />
| September 12th, 2019 <br />
|-<br />
| 2.7.11<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-javadoc.jar jar]<br />
| July 25th, 2019 <br />
|-<br />
| 2.7.10<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-javadoc.jar jar]<br />
| February 11th, 2019 <br />
|-<br />
| 2.7.9<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-javadoc.jar jar]<br />
| December 12th, 2018 <br />
|-<br />
| 2.7.8<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-javadoc.jar jar]<br />
| September 3rd, 2018 <br />
|-<br />
| 2.7.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-javadoc.jar jar]<br />
| May 18th, 2018 <br />
|-<br />
| 2.7.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-javadoc.jar jar]<br />
| March 23rd, 2018 <br />
|-<br />
| 2.7.5<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-javadoc.jar jar]<br />
| November 10th, 2017 <br />
|-<br />
| 2.7.4<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-javadoc.jar jar]<br />
| July 29th, 2017 <br />
|-<br />
| 2.7.3<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-javadoc.jar jar]<br />
| December 12th, 2016 <br />
|-<br />
| 2.7.2<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-javadoc.jar jar]<br />
| May 20th, 2016 <br />
|-<br />
| 2.7.1<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-javadoc.jar jar]<br />
| May 20th, 2016 <br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/><br />
<br />
==== Alida in C++ ====<br />
Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]).<br> Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=346Main Page2021-04-09T08:56:48Z<p>Moeller: /* Alida - Advanced Library for Integrated Development of Data Analysis Applications */</p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top; width:65%;"" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
<!--<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
--><br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top;width:35%;" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 3.0.2 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 04/2021: Alida 3.0.2 has been released coming with a more fancy handling of parameters on command line resulting in full support for dynamic operator interfaces from command line.<br />
* 05/2020: Alida 3.0 has been released!<br> The main novelty is a change in the online help system which was formerly based on the [https://de.wikipedia.org/wiki/JavaHelp_System Java Help System] and now relies on operator class annotations.<br />
* 07/2019: Alida 2.7.11 has been released.<br />
* 02/2019: Alida 2.7.10 has been released.<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Gnu PGP Public Key'''<br><br />
Since version 2.7.4 Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=345Main Page2021-04-09T08:48:07Z<p>Moeller: /* Alida - Advanced Library for Integrated Development of Data Analysis Applications */</p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top; width:65%;"" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
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'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
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<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top;width:35%;" |<br />
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<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 3.0.2 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
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'''Latest News'''<br><br />
* 04/2021: Alida 3.0.2 has been released coming with a more fancy handling of parameters on command line resulting in full support for dynamic operator interfaces from command line.<br />
* 05/2020: Alida 3.0 has been released!<br> The main novelty is a change in the online help system which was formerly based on the [https://de.wikipedia.org/wiki/JavaHelp_System Java Help System] and now relies on operator class annotations.<br />
* 07/2019: Alida 2.7.11 has been released.<br />
* 02/2019: Alida 2.7.10 has been released.<br />
The news archive can be found [[NewsArchive | here]].<br />
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'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
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'''Gnu PGP Public Key'''<br><br />
Since version 2.7.4 Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
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'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=344Downloads2020-05-26T10:49:28Z<p>Moeller: /* Long-term archival of major releases */</p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 3.0.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archival of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://doi.org/10.5281/zenodo.3855411 Alida 3.0], [[Image:zenodo.3855411.svg.png|165px|link=https://doi.org/10.5281/zenodo.3855411]]<br><br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.47586]]<br><br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 3.0<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-javadoc.jar jar]<br />
| May 15th, 2020 <br />
|-<br />
| 2.7.13<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-javadoc.jar jar]<br />
| February 20th, 2020 <br />
|-<br />
| 2.7.12<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-javadoc.jar jar]<br />
| September 12th, 2019 <br />
|-<br />
| 2.7.11<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-javadoc.jar jar]<br />
| July 25th, 2019 <br />
|-<br />
| 2.7.10<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-javadoc.jar jar]<br />
| February 11th, 2019 <br />
|-<br />
| 2.7.9<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-javadoc.jar jar]<br />
| December 12th, 2018 <br />
|-<br />
| 2.7.8<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-javadoc.jar jar]<br />
| September 3rd, 2018 <br />
|-<br />
| 2.7.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-javadoc.jar jar]<br />
| May 18th, 2018 <br />
|-<br />
| 2.7.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-javadoc.jar jar]<br />
| March 23rd, 2018 <br />
|-<br />
| 2.7.5<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-javadoc.jar jar]<br />
| November 10th, 2017 <br />
|-<br />
| 2.7.4<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-javadoc.jar jar]<br />
| July 29th, 2017 <br />
|-<br />
| 2.7.3<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-javadoc.jar jar]<br />
| December 12th, 2016 <br />
|-<br />
| 2.7.2<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-javadoc.jar jar]<br />
| May 20th, 2016 <br />
|-<br />
| 2.7.1<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-javadoc.jar jar]<br />
| May 20th, 2016 <br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=File:Zenodo.3855411.svg.png&diff=343File:Zenodo.3855411.svg.png2020-05-26T10:48:35Z<p>Moeller: </p>
<hr />
<div></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=342Downloads2020-05-26T10:47:25Z<p>Moeller: /* Long-term archival of major releases */</p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 3.0.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archival of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://doi.org/10.5281/zenodo.3855411 Alida 3.0], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.3855411]]<br><br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.47586]]<br><br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 3.0<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-javadoc.jar jar]<br />
| May 15th, 2020 <br />
|-<br />
| 2.7.13<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-javadoc.jar jar]<br />
| February 20th, 2020 <br />
|-<br />
| 2.7.12<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-javadoc.jar jar]<br />
| September 12th, 2019 <br />
|-<br />
| 2.7.11<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-javadoc.jar jar]<br />
| July 25th, 2019 <br />
|-<br />
| 2.7.10<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-javadoc.jar jar]<br />
| February 11th, 2019 <br />
|-<br />
| 2.7.9<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-javadoc.jar jar]<br />
| December 12th, 2018 <br />
|-<br />
| 2.7.8<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-javadoc.jar jar]<br />
| September 3rd, 2018 <br />
|-<br />
| 2.7.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-javadoc.jar jar]<br />
| May 18th, 2018 <br />
|-<br />
| 2.7.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-javadoc.jar jar]<br />
| March 23rd, 2018 <br />
|-<br />
| 2.7.5<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-javadoc.jar jar]<br />
| November 10th, 2017 <br />
|-<br />
| 2.7.4<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-javadoc.jar jar]<br />
| July 29th, 2017 <br />
|-<br />
| 2.7.3<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-javadoc.jar jar]<br />
| December 12th, 2016 <br />
|-<br />
| 2.7.2<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-javadoc.jar jar]<br />
| May 20th, 2016 <br />
|-<br />
| 2.7.1<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-javadoc.jar jar]<br />
| May 20th, 2016 <br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Projects&diff=341Projects2020-05-16T07:59:20Z<p>Moeller: /* Related Projects */</p>
<hr />
<div>== Related Projects ==<br />
<br />
* '''''MiToBo - A microscope image analysis toolbox'''''<br>Webpage: [https://mitobo.informatik.uni-halle.de https://mitobo.informatik.uni-halle.de]<br />
<br />
== Publications ==<br />
<br />
* S. Posch and B. Möller, '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''',<br> Journal of Open Research Software, 5(1):7, DOI: http://doi.org/10.5334/jors.124, 2017.<br />
* S. Posch and B. Möller, '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms''''',<br> Pattern Recognition and Image Analysis, ISSN 1054-6618, Vol. 26, No. 1, pp. 181-189, 2016.<br />
<br />
* S. Posch and B. Möller, '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms''''',<br> 9th Open German-Russian Workshop on Pattern Recognition and Image Understanding (OGRW), Electronic on-site Proceedings, Koblenz, Germany, December 2014.<br />
<br />
* B. Möller and S. Posch, '''''A Framework Unifying the Development of Image Analysis Algorithms and Associated User Interfaces''''',<br> In Proc. of 13th IAPR International Conference on Machine Vision Applications (MVA '13), pp. 447-450, Kyoto, Japan, May 2013.<br />
<br />
* S. Kirchner, S. Posch and B. Möller, '''''Graphical Programming in Alida and ImageJ 2.0 with Grappa''''',<br> In Proc. of ImageJ User & Developer Conference, pp. 138-143, ISBN 2-919941-18-6, Mondorf-les-Bains, Luxembourg, October 2012. <br />
<br />
* S. Posch and B. Möller, '''''Automatic Generation of Processing Histories using Alida''''',<br> In Proc. of ImageJ User & Developer Conference, pp. 218-221, ISBN 2-919941-18-6, Mondorf-les-Bains, Luxembourg, October 2012.<br> This contribution was awarded as the "Best Scientific Poster" of the ImageJ conference!<br />
<br />
* S. Posch and B. Möller, '''''Alida - Automatic Generation of User Interfaces for Data Analysis Algorithms''''',<br> Poster presentation at IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI), Bioimage Analysis Workshop , Barcelona, Spain, April 2012.<br />
<br />
* B. Möller, O. Greß and S. Posch, '''''Knowing what happened - Automatic Documentation of Image Analysis Processes''''',<br> In Proc. of 8th International Conference on Computer Vision Systems (ICVS '11), J.L. Crowley, B.A. Draper, and M. Thonnat (Eds.),<br> Springer, LNCS 6962, pp. 1-10. Inria Sophia Antipolis, France, September 2011.</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=340Downloads2020-05-16T07:57:45Z<p>Moeller: </p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 3.0.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archival of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.47586]]<br><br />
<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 3.0<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-javadoc.jar jar]<br />
| May 15th, 2020 <br />
|-<br />
| 2.7.13<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-javadoc.jar jar]<br />
| February 20th, 2020 <br />
|-<br />
| 2.7.12<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-javadoc.jar jar]<br />
| September 12th, 2019 <br />
|-<br />
| 2.7.11<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-javadoc.jar jar]<br />
| July 25th, 2019 <br />
|-<br />
| 2.7.10<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-javadoc.jar jar]<br />
| February 11th, 2019 <br />
|-<br />
| 2.7.9<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-javadoc.jar jar]<br />
| December 12th, 2018 <br />
|-<br />
| 2.7.8<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-javadoc.jar jar]<br />
| September 3rd, 2018 <br />
|-<br />
| 2.7.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-javadoc.jar jar]<br />
| May 18th, 2018 <br />
|-<br />
| 2.7.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-javadoc.jar jar]<br />
| March 23rd, 2018 <br />
|-<br />
| 2.7.5<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-javadoc.jar jar]<br />
| November 10th, 2017 <br />
|-<br />
| 2.7.4<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-javadoc.jar jar]<br />
| July 29th, 2017 <br />
|-<br />
| 2.7.3<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-javadoc.jar jar]<br />
| December 12th, 2016 <br />
|-<br />
| 2.7.2<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-javadoc.jar jar]<br />
| May 20th, 2016 <br />
|-<br />
| 2.7.1<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-javadoc.jar jar]<br />
| May 20th, 2016 <br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=339Main Page2020-05-16T07:46:27Z<p>Moeller: </p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top; width:65%;"" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top;width:35%;" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 3.0 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 05/2020: Alida 3.0 has been released!<br> The main novelty is a change in the online help system which was formerly based on the [https://de.wikipedia.org/wiki/JavaHelp_System Java Help System] and now relies on operator class annotations.<br />
* 07/2019: Alida 2.7.11 has been released.<br />
* 02/2019: Alida 2.7.10 has been released.<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Gnu PGP Public Key'''<br><br />
Since version 2.7.4 Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=NewsArchive&diff=338NewsArchive2020-05-16T07:45:36Z<p>Moeller: </p>
<hr />
<div>== News Archive ==<br />
<br />
* 12/2018: <br>Alida 2.7.9 has been released.<br />
<br />
* 09/2018: <br>Alida 2.7.8 has been released.<br />
<br />
* 05/2018: <br>Alida 2.7.7 has been released.<br />
<br />
* 03/2018: <br>Alida 2.7.6 has been released.<br />
<br />
* 01/2018: <br>Alida 2.7.5.1 has been released.<br />
<br />
* 11/2017: <br>Alida 2.7.5 has been released. The mechanism to store parameters of operators is now more flexible and correctly handles the visibility of static and dynamic parameters.<br />
<br />
* 07/2017: <br>Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
<br />
* 03/2017: <br>A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
<br />
* 03/2016: <br>Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
<br />
* 06/2015: <br>Alida's sources are now available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
* 06/2015: <br>Alida 2.6 has been released.<br />
<br />
* 03/30/2015: <br>Release of version 2.5.<br> Alida now supports callback functions attached to parameters which are called upon changes of the values of the parameters. This, e.g., allows for dynamic updates of the set of parameters of an operator and for dynamic configuration of the GUI.<br />
<br />
* 01/07/2015: <br>Release of version 2.4.4.<br />
<br />
* 12/04/2014: <br>Alida and in particular its technical ingredients will be presented at the '''OGRW 2014''', which is the 9th Open German-Russian Workshop on Pattern Recognition and Image Understanding.<br> The title of the contribution is '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms'''''.<br> The workshop is taking place this week in Koblenz/Germany.<br />
<br />
* 12/01/2014: <br>Release of version 2.4.3.<br />
<br />
* 07/25/2014: <br>Release of version 2.4.2<br> Some more bugfixes.<br />
<br />
* 07/18/2014: <br>Release of version 2.4.1<br> Bugfixed an annoying problem with keyboard shortcuts.<br />
<br />
* 06/29/2014: <br>Release of version 2.4.<br> Main new feature is the support for progress events of operators. In addition, numerous bugfixes and enhancements in the graphical user interfaces are included.<br />
<br />
* 01/31/2014: <br>Release of version 2.3.1.<br> A serious bug in saving and loading workflows and operator configurations was fixed.<br />
<br />
* 01/17/2014: <br>Release of version 2.3.<br> The project management of the Alida Java project has switched to Maven, i.e. from now on Alida can be downloaded directly from our Maven server.<br> The new release by itself mainly includes bugfixes in the core of Alida improving the stability. <br />
<br />
* 05/17/2013: <br> Alida will be presented at the '''MVA 2013''', which is the Thirteenth IAPR International Conference on Machine Vision Applications.<br> The title of the contribution is '''''A Framework Unifying the Development of Image Analysis Algorithms and Associated User Interfaces'''''.<br> The conference will take place in Kyoto/Japan from May 21st to 23rd. We hope to meet you there!<br />
<br />
* 05/17/2013: <br>Release of version 2.2.<br> Grappa has increased its user-friendliness by supporting key shortcuts now. In addition, the mechanism to save and load configurations in Alida<br> has switched from the Java serialization framework to XML beans. Finally, many bugfixes in Alida's core were again applied.<br />
<br />
* 02/28/2013: <br>Release of version 2.1.<br> The new release includes many bugfixes in Alida's core improving the stability, and minor improvements regarding layout and handling of Alida's user interfaces.<br> Note that also a new version of the manual was released which now covers all important aspects of programming with Alida.<br />
<br />
* 12/20/2012: <br>Release of version 2.0.<br> This version includes the graphical editor '''Grappa''' to compose workflows of operators.<br />
<br />
* 11/10/2012: <br> Updated version of Chipory available for download.<br />
<br />
* 26/07/2012: <br> Alida will be presented at the '''''ImageJ User & Developer Conference 2012''''' to be held at the end of October in Mondorf-les-Bains, Luxembourg.<br> There will be a poster presentation combined with a demo entitled [http://imagejconf.tudor.lu/program/poster/birgit_moeller996310491 '''Automatic Generation of Processing Histories using Alida'''].<br> It will provide an introduction to the processing history mechanism implemented in Alida, and its usage.<br> Also a talk will be given about our new graphical editor ''Grappa'' entitled '''Graphical Programming in Alida and ImageJ 2.0 with Grappa'''.<br />
<br />
* 12/07/2012: <br>New release of chipory ready for download<br />
<br />
* 21/03/2012:<br> Alida will be presented at the '''''IEEE International Symposium on Biomedical Imaging (ISBI)''''' to be held at the end of April in Barcelona.<br> There will be a poster presentation combined with a demo at the '''''Bioimage Analysis Workshop on Open Source Software''''' held in conjunction with ISBI.<br> The title will be '''ALIDA - Automatic generation of user interfaces for data analysis algorithms'''.<br />
<br />
* 12/03/2012:<br> The Alida concept now features a prototypical implementation in C++! It supports generic operator execution from command line.<br>Release 0.1 is available now from the download page.<br />
<br />
* 02/03/2012:<br>Alida release 1.2 has just been published! You can get the new version in the download section!<br>Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=MediaWiki:Sidebar&diff=337MediaWiki:Sidebar2020-02-24T19:33:24Z<p>Moeller: </p>
<hr />
<div>* navigation<br />
** mainpage|mainpage-description<br />
** features|Features<br />
** Screenshots|Screenshots<br />
** Downloads|Downloads<br />
** Installation|Installation<br />
** Support|Support<br />
** Quickstart|Quickstart and Code Examples<br />
** Projects|Related Projects and Publications<br />
** Acknowledge|Acknowledgements<br />
** Alida:About|Imprint<br />
* documentation<br />
** http://alida.informatik.uni-halle.de/downloads/manual/AlidaManual.pdf|Manual<br />
** http://alida.informatik.uni-halle.de/api/java/index.html|Javadoc API<br />
** frequently_asked_questions|FAQs<br />
* development<br />
** https://github.com/alida-hub/alida|Code on Github<br />
** https://github.com/alida-hub/alida/issues|Issue tracking<br />
* SEARCH<br />
* TOOLBOX<br />
* LANGUAGES</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=336Main Page2019-07-31T10:45:18Z<p>Moeller: /* Alida - Advanced Library for Integrated Development of Data Analysis Applications */</p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top; width:65%;"" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top;width:35%;" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.11 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 07/2019: Alida 2.7.11 has been released.<br />
* 02/2019: Alida 2.7.10 has been released.<br />
* 12/2018: Alida 2.7.9 has been released.<br />
* 09/2018: Alida 2.7.8 has been released.<br />
* 05/2018: Alida 2.7.7 has been released.<br />
* 03/2018: Alida 2.7.6 has been released.<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Gnu PGP Public Key'''<br><br />
Since version 2.7.4 Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=NewsArchive&diff=335NewsArchive2019-07-31T10:45:03Z<p>Moeller: /* News Archive */</p>
<hr />
<div>== News Archive ==<br />
<br />
* 01/2018: <br>Alida 2.7.5.1 has been released.<br />
<br />
* 11/2017: <br>Alida 2.7.5 has been released. The mechanism to store parameters of operators is now more flexible and correctly handles the visibility of static and dynamic parameters.<br />
<br />
* 07/2017: <br>Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
<br />
* 03/2017: <br>A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
<br />
* 03/2016: <br>Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
<br />
* 06/2015: <br>Alida's sources are now available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
* 06/2015: <br>Alida 2.6 has been released.<br />
<br />
* 03/30/2015: <br>Release of version 2.5.<br> Alida now supports callback functions attached to parameters which are called upon changes of the values of the parameters. This, e.g., allows for dynamic updates of the set of parameters of an operator and for dynamic configuration of the GUI.<br />
<br />
* 01/07/2015: <br>Release of version 2.4.4.<br />
<br />
* 12/04/2014: <br>Alida and in particular its technical ingredients will be presented at the '''OGRW 2014''', which is the 9th Open German-Russian Workshop on Pattern Recognition and Image Understanding.<br> The title of the contribution is '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms'''''.<br> The workshop is taking place this week in Koblenz/Germany.<br />
<br />
* 12/01/2014: <br>Release of version 2.4.3.<br />
<br />
* 07/25/2014: <br>Release of version 2.4.2<br> Some more bugfixes.<br />
<br />
* 07/18/2014: <br>Release of version 2.4.1<br> Bugfixed an annoying problem with keyboard shortcuts.<br />
<br />
* 06/29/2014: <br>Release of version 2.4.<br> Main new feature is the support for progress events of operators. In addition, numerous bugfixes and enhancements in the graphical user interfaces are included.<br />
<br />
* 01/31/2014: <br>Release of version 2.3.1.<br> A serious bug in saving and loading workflows and operator configurations was fixed.<br />
<br />
* 01/17/2014: <br>Release of version 2.3.<br> The project management of the Alida Java project has switched to Maven, i.e. from now on Alida can be downloaded directly from our Maven server.<br> The new release by itself mainly includes bugfixes in the core of Alida improving the stability. <br />
<br />
* 05/17/2013: <br> Alida will be presented at the '''MVA 2013''', which is the Thirteenth IAPR International Conference on Machine Vision Applications.<br> The title of the contribution is '''''A Framework Unifying the Development of Image Analysis Algorithms and Associated User Interfaces'''''.<br> The conference will take place in Kyoto/Japan from May 21st to 23rd. We hope to meet you there!<br />
<br />
* 05/17/2013: <br>Release of version 2.2.<br> Grappa has increased its user-friendliness by supporting key shortcuts now. In addition, the mechanism to save and load configurations in Alida<br> has switched from the Java serialization framework to XML beans. Finally, many bugfixes in Alida's core were again applied.<br />
<br />
* 02/28/2013: <br>Release of version 2.1.<br> The new release includes many bugfixes in Alida's core improving the stability, and minor improvements regarding layout and handling of Alida's user interfaces.<br> Note that also a new version of the manual was released which now covers all important aspects of programming with Alida.<br />
<br />
* 12/20/2012: <br>Release of version 2.0.<br> This version includes the graphical editor '''Grappa''' to compose workflows of operators.<br />
<br />
* 11/10/2012: <br> Updated version of Chipory available for download.<br />
<br />
* 26/07/2012: <br> Alida will be presented at the '''''ImageJ User & Developer Conference 2012''''' to be held at the end of October in Mondorf-les-Bains, Luxembourg.<br> There will be a poster presentation combined with a demo entitled [http://imagejconf.tudor.lu/program/poster/birgit_moeller996310491 '''Automatic Generation of Processing Histories using Alida'''].<br> It will provide an introduction to the processing history mechanism implemented in Alida, and its usage.<br> Also a talk will be given about our new graphical editor ''Grappa'' entitled '''Graphical Programming in Alida and ImageJ 2.0 with Grappa'''.<br />
<br />
* 12/07/2012: <br>New release of chipory ready for download<br />
<br />
* 21/03/2012:<br> Alida will be presented at the '''''IEEE International Symposium on Biomedical Imaging (ISBI)''''' to be held at the end of April in Barcelona.<br> There will be a poster presentation combined with a demo at the '''''Bioimage Analysis Workshop on Open Source Software''''' held in conjunction with ISBI.<br> The title will be '''ALIDA - Automatic generation of user interfaces for data analysis algorithms'''.<br />
<br />
* 12/03/2012:<br> The Alida concept now features a prototypical implementation in C++! It supports generic operator execution from command line.<br>Release 0.1 is available now from the download page.<br />
<br />
* 02/03/2012:<br>Alida release 1.2 has just been published! You can get the new version in the download section!<br>Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=334Downloads2019-06-04T10:08:56Z<p>Moeller: </p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.10.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archival of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.47586]]<br><br />
<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=331Main Page2018-01-31T15:59:14Z<p>Moeller: </p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top; width:65%;"" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top;width:35%;" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.5.1 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 01/2018: Alida 2.7.5.1 has been released.<br />
* 11/2017: Alida 2.7.5 has been released. The mechanism to store parameters of operators is now more flexible and correctly handles the visibility of static and dynamic parameters.<br />
* 07/2017: Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Gnu PGP Public Key'''<br><br />
Since version 2.7.4 Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=330Main Page2018-01-31T15:50:48Z<p>Moeller: </p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.5.1 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 01/2018: Alida 2.7.5.1 has been released.<br />
* 11/2017: Alida 2.7.5 has been released. The mechanism to store parameters of operators is now more flexible and correctly handles the visibility of static and dynamic parameters.<br />
* 07/2017: Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=NewsArchive&diff=329NewsArchive2018-01-31T15:50:38Z<p>Moeller: /* News Archive */</p>
<hr />
<div>== News Archive ==<br />
<br />
* 03/2017: A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
<br />
* 03/2016: Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
<br />
* 06/2015: Alida's sources are now available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
* 06/2015: Alida 2.6 has been released.<br />
<br />
* 03/30/2015: <br>Release of version 2.5.<br> Alida now supports callback functions attached to parameters which are called upon changes of the values of the parameters. This, e.g., allows for dynamic updates of the set of parameters of an operator and for dynamic configuration of the GUI.<br />
<br />
* 01/07/2015: <br>Release of version 2.4.4.<br />
<br />
* 12/04/2014: <br>Alida and in particular its technical ingredients will be presented at the '''OGRW 2014''', which is the 9th Open German-Russian Workshop on Pattern Recognition and Image Understanding.<br> The title of the contribution is '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms'''''.<br> The workshop is taking place this week in Koblenz/Germany.<br />
<br />
* 12/01/2014: <br>Release of version 2.4.3.<br />
<br />
* 07/25/2014: <br>Release of version 2.4.2<br> Some more bugfixes.<br />
<br />
* 07/18/2014: <br>Release of version 2.4.1<br> Bugfixed an annoying problem with keyboard shortcuts.<br />
<br />
* 06/29/2014: <br>Release of version 2.4.<br> Main new feature is the support for progress events of operators. In addition, numerous bugfixes and enhancements in the graphical user interfaces are included.<br />
<br />
* 01/31/2014: <br>Release of version 2.3.1.<br> A serious bug in saving and loading workflows and operator configurations was fixed.<br />
<br />
* 01/17/2014: <br>Release of version 2.3.<br> The project management of the Alida Java project has switched to Maven, i.e. from now on Alida can be downloaded directly from our Maven server.<br> The new release by itself mainly includes bugfixes in the core of Alida improving the stability. <br />
<br />
* 05/17/2013: <br> Alida will be presented at the '''MVA 2013''', which is the Thirteenth IAPR International Conference on Machine Vision Applications.<br> The title of the contribution is '''''A Framework Unifying the Development of Image Analysis Algorithms and Associated User Interfaces'''''.<br> The conference will take place in Kyoto/Japan from May 21st to 23rd. We hope to meet you there!<br />
<br />
* 05/17/2013: <br>Release of version 2.2.<br> Grappa has increased its user-friendliness by supporting key shortcuts now. In addition, the mechanism to save and load configurations in Alida<br> has switched from the Java serialization framework to XML beans. Finally, many bugfixes in Alida's core were again applied.<br />
<br />
* 02/28/2013: <br>Release of version 2.1.<br> The new release includes many bugfixes in Alida's core improving the stability, and minor improvements regarding layout and handling of Alida's user interfaces.<br> Note that also a new version of the manual was released which now covers all important aspects of programming with Alida.<br />
<br />
* 12/20/2012: <br>Release of version 2.0.<br> This version includes the graphical editor '''Grappa''' to compose workflows of operators.<br />
<br />
* 11/10/2012: <br> Updated version of Chipory available for download.<br />
<br />
* 26/07/2012: <br> Alida will be presented at the '''''ImageJ User & Developer Conference 2012''''' to be held at the end of October in Mondorf-les-Bains, Luxembourg.<br> There will be a poster presentation combined with a demo entitled [http://imagejconf.tudor.lu/program/poster/birgit_moeller996310491 '''Automatic Generation of Processing Histories using Alida'''].<br> It will provide an introduction to the processing history mechanism implemented in Alida, and its usage.<br> Also a talk will be given about our new graphical editor ''Grappa'' entitled '''Graphical Programming in Alida and ImageJ 2.0 with Grappa'''.<br />
<br />
* 12/07/2012: <br>New release of chipory ready for download<br />
<br />
* 21/03/2012:<br> Alida will be presented at the '''''IEEE International Symposium on Biomedical Imaging (ISBI)''''' to be held at the end of April in Barcelona.<br> There will be a poster presentation combined with a demo at the '''''Bioimage Analysis Workshop on Open Source Software''''' held in conjunction with ISBI.<br> The title will be '''ALIDA - Automatic generation of user interfaces for data analysis algorithms'''.<br />
<br />
* 12/03/2012:<br> The Alida concept now features a prototypical implementation in C++! It supports generic operator execution from command line.<br>Release 0.1 is available now from the download page.<br />
<br />
* 02/03/2012:<br>Alida release 1.2 has just been published! You can get the new version in the download section!<br>Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=328Downloads2018-01-31T15:46:08Z<p>Moeller: /* Current Java release */</p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.5.1.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archival of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.47586]]<br><br />
<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=327Main Page2018-01-31T15:45:48Z<p>Moeller: /* Alida - Advanced Library for Integrated Development of Data Analysis Applications */</p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.5.1 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 01/2018: Alida 2.7.5.1 has been released.<br />
* 11/2017: Alida 2.7.5 has been released. The mechanism to store parameters of operators is now more flexible and correctly handles the visibility of static and dynamic parameters.<br />
* 07/2017: Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
* 03/2017: A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
* 03/2016: Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=326Main Page2017-11-10T15:05:06Z<p>Moeller: /* Alida - Advanced Library for Integrated Development of Data Analysis Applications */</p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
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'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
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'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
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'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
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'''How to get Alida?'''<br><br />
* You can download Alida 2.7.5 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
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'''Latest News'''<br><br />
* 11/2017: Alida 2.7.5 has been released. The mechanism to store parameters of operators is now more flexible and correctly handles the visibility of static and dynamic parameters.<br />
* 07/2017: Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
* 03/2017: A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
* 03/2016: Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
The news archive can be found [[NewsArchive | here]].<br />
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'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
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'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
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|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=325Downloads2017-11-10T15:02:54Z<p>Moeller: </p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.5.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
<br />
==== Long-term archival of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.47586]]<br><br />
<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
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! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=324Main Page2017-09-04T12:36:18Z<p>Moeller: </p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/alida-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.4 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 07/2017: Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
* 03/2017: A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
* 03/2016: Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=323Main Page2017-09-04T12:36:00Z<p>Moeller: </p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|100px|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.4 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 07/2017: Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
* 03/2017: A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
* 03/2016: Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=322Main Page2017-09-04T12:35:06Z<p>Moeller: </p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/Alida ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.4 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 07/2017: Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
* 03/2017: A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
* 03/2016: Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=321Main Page2017-09-04T12:34:05Z<p>Moeller: </p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Visit Alida also at...'''<br><br />
{|<br />
|style="text-align:center;width:10%"|[[file:90px-Imagej-128.png|90px|link=http://imagej.net/MiToBo]]<br />
|style="text-align:center;width:10%"|[[file:90px-Git.png|90px|link=https://github.com/mitobo-hub]]<br />
|-<br />
|style="text-align:center;width:10%"|[http://imagej.net/MiToBo ImageJ.net]<br />
|style="text-align:center;width:10%"|[https://github.com/mitobo-hub GitHub]<br />
|}<br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.4 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 07/2017: Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
* 03/2017: A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
* 03/2016: Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=File:90px-Imagej-128.png&diff=320File:90px-Imagej-128.png2017-09-04T12:33:13Z<p>Moeller: </p>
<hr />
<div></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=File:90px-Git.png&diff=319File:90px-Git.png2017-09-04T12:33:02Z<p>Moeller: </p>
<hr />
<div></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=318Downloads2017-07-31T13:46:17Z<p>Moeller: </p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.4.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
<br />
==== Long-term archival of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.47586]]<br><br />
<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=317Downloads2017-07-31T13:44:58Z<p>Moeller: /* Long-term archiving of major releases */</p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.4.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archival of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|175px|link=https://doi.org/10.5281/zenodo.47586]]<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=316Downloads2017-07-31T13:44:33Z<p>Moeller: /* Long-term archiving of major releases */</p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.4.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archiving of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|175px|link=https://doi.org/10.5281/zenodo.47586]]<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=315Downloads2017-07-31T13:44:03Z<p>Moeller: /* Long-term archiving of major releases */</p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.4.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archiving of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], DOI: [[Image:zenodo.47586.svg.png|200px|link=https://doi.org/10.5281/zenodo.47586]]<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=File:Zenodo.47586.svg.png&diff=314File:Zenodo.47586.svg.png2017-07-31T13:43:49Z<p>Moeller: </p>
<hr />
<div></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=313Downloads2017-07-31T13:43:40Z<p>Moeller: </p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.4.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archiving of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], DOI: [[Image:zenodo.47586.png|200px|link=https://doi.org/10.5281/zenodo.47586]]<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=File:Zenodo.47586.png&diff=312File:Zenodo.47586.png2017-07-31T13:40:54Z<p>Moeller: </p>
<hr />
<div></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=311Downloads2017-07-31T13:39:56Z<p>Moeller: /* Long-term archiving of major releases */</p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.4.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archiving of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], DOI:<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=310Downloads2017-07-31T13:37:27Z<p>Moeller: </p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.4.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Long-term archiving of major releases ====<br />
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations:<br />
* [https://zenodo.org/record/47586 Alida 2.7], https://zenodo.org/badge/DOI/10.5281/zenodo.47586.svg<br />
<br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Downloads&diff=309Downloads2017-07-31T13:26:17Z<p>Moeller: /* Current Java release */</p>
<hr />
<div>Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found [[CPlusPlus|here]]). Note that only the Java version is currently under active development and maintenance. The C++ implementation is in a rather early state lacking lots of features.<br />
<br><br />
<br />
==== Current Java release ====<br />
<br />
The current release of Alida is 2.7.4.<br />
<br />
Since release 2.3 we support Maven for managing Alida's project resources.<br> You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:<br />
<br />
[https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida]<br />
<br />
For download the following files are of interest:<br />
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)<br />
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)<br />
* API: the Alida Javadoc API (jar format)<br><br />
<br />
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
<!--<br />
Amongst others you can find there...<br />
* ... the Alida Distribution including documentation, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-bin.zip]<br />
* ... the binaries only, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4.jar]<br />
* ... the Alida API, Release 2.4.4: [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.4.4/alida-2.4.4-javadoc.jar]<br />
--><br />
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br><br />
<br />
==== Using Alida in your own code ====<br />
<br />
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.<br> Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:<br />
<br />
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] <br />
<br />
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.<br> The project already defines all repositories and dependencies required to use Alida's functionality.<br><br />
<br />
==== Manual ====<br />
<br />
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. <br />
<br />
* Alida-Manual, Version 2.7 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (March 2016)<br />
<br/><br />
<br />
==== Additional resources ====<br />
<br />
* '''Chipory''' - a graph visualization tool for displaying MiToBo history graphs<br/>Chipory is an extended version of the [http://www.cs.bilkent.edu.tr/~ivis/chisio.html Chisio software] developed at the Bilkent University in Turkey.<br />
<br/><br />
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.<br />
<br />
* To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.<BR><br />
* In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.<BR><br />
* For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.<br />
<br/><br />
Download the current release as of 7-12-2012:<br />
* Chipory binary [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Chipory.zip zip]<br />
* self extracting installer for Windows [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/chipory-setup.exe chipory-setup.exe]<br />
Source code for Chipory is available upon request.<br />
<br/><br />
<br />
==== Logos ====<br />
<br />
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF]<br />
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF]<br />
<br><br />
<br />
==== Release Archive (>= 2.3) ====<br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Distribution<br />
! Binaries only <br />
! API <br />
! Date<br />
|-<br />
| 2.7<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar]<br />
| March 15th, 2016 <br />
|-<br />
| 2.6<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar]<br />
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar]<br />
| June 17th, 2015 <br />
|-<br />
| 2.5<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar]<br />
| March 30th, 2015 (Callbacks)<br />
|-<br />
| 2.4.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar]<br />
| Jan 7th, 2015<br />
|-<br />
| 2.4.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar]<br />
| Dec 1st, 2014<br />
|-<br />
| 2.4.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar]<br />
| Jul 25th, 2014<br />
|-<br />
| 2.4.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar]<br />
| Jul 18th, 2014<br />
|-<br />
| 2.4<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar]<br />
| Jun 29th, 2014<br />
|-<br />
| 2.3.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar]<br />
| Jan 31st, 2014<br />
|-<br />
| 2.3<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar]<br />
| Jan 16th, 2014<br />
|}<br />
<br><br />
<br />
==== Release Archive (< 2.3) ====<br />
<br />
In the pre-Maven era Alida's dependencies on external jars had to be managed manually.<br />
Alida required some external jars included in the Alida binary zipfiles (since v2.0).<br />
<br />
For earlier versions the following external jars are needed to use Alida:<br />
<br />
* [http://xmlbeans.apache.org/ XMLBeans], Version 2.5.0<br />
* [http://xstream.codehaus.org/ XStream], Version 1.3.1<br />
* [http://javahelp.java.net/ JavaHelp], Version 2.0_05<br />
<br />
In addition, Alida requires some more libraries which are in-house developments:<br />
<br />
* Alida requires some graphml extensions to be found in '''''aldgraphml.jar'''''.<br />
* Since release 2.2 saving and loading of configurations is based on XML beans, hence Alida requires some additional xml packages to be found in '''''alida-xmlprovider.jar'''''.<br />
* The graphical operator runner features an online help system based on [http://javahelp.java.net/ JavaHelp System] which is included in '''Alida-Help.jar'''.<br />
<br />
If you download the Alida binary zipfile you will find these two libraries in the subdirectory ''intjars'' of the zipfile.<br/> Make sure that all of them are in the classpath when executing the operator runners.<br/><br />
<br />
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%"<br />
! Version <br />
! Binaries <br />
! Sources <br />
! API <br />
! Date<br />
|-<br />
| 2.2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.1.zip zip]<br />
| May 17th, 2013 (Bugfix Release)<br />
|-<br />
|-<br />
| 2.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.2.zip zip]<br />
| May 17th, 2013<br />
|-<br />
| 2.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-v2.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-v2.1.zip zip]<br />
| February 28th, 2013<br />
|-<br />
| 2.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-2.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-2.0.zip zip]<br />
| December 20th, 2012<br />
|-<br />
| 1.2<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.2.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.2.zip zip]<br />
| March 2nd, 2012<br />
|-<br />
| 1.1<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.1.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.1.zip zip]<br />
| Sep 14th, 2011<br />
|-<br />
| 1.0<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_bin-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_src-1.0.zip zip]<br />
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida_api-1.0.zip zip]<br />
| May 9th, 2011<br />
|}<br />
<br/></div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=308Main Page2017-07-31T13:25:46Z<p>Moeller: /* Alida - Advanced Library for Integrated Development of Data Analysis Applications */</p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.4 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 07/2017: Alida 2.7.4 has been released.<br>From now on Alida releases are PGP signed. Alida's [https://pgp.mit.edu/pks/lookup?op=get&search=0x72C17EF19A4D2F66 public key] for verification can be found on public key servers, e.g., at https://pgp.mit.edu/. <br />
* 03/2017: A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
* 03/2016: Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Frequently_asked_questions&diff=307Frequently asked questions2017-03-28T08:25:49Z<p>Moeller: </p>
<hr />
<div>== How to cite Alida? ==<br />
If you use the Alida library as basis for your own projects, please cite one of our main papers in your publications:<br />
* S. Posch and B. Möller, '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''',<br> Journal of Open Research Software, 5(1):7, DOI: http://doi.org/10.5334/jors.124, 2017.<br />
* S. Posch and B. Möller, '''''Design and implementation of the Alida framework to ease the development of image analysis algorithms''''',<br> Pattern Recognition and Image Analysis, 26(1):181-189, 2016.<br />
* B. Möller and S. Posch, '''''A Framework Unifying the Development of Image Analysis Algorithms and Associated User Interfaces''''',<br> Proc. of 13th IAPR International Conference on Machine Vision Applications (MVA '13), pp. 447-450, Kyoto, Japan, May 2013.<br />
* B. Möller, O. Greß and S. Posch, '''''Knowing what happened - Automatic Documentation of Image Analysis Processes''''',<br> Proc. of 8th International Conference on Computer Vision Systems (ICVS '11), J.L. Crowley, B.A. Draper, and M. Thonnat (Eds.),<br> Springer, LNCS 6962, pp. 1-10. Inria Sophia Antipolis, France, September 2011.<br />
<br />
More publications can be found [http://www2.informatik.uni-halle.de/agprbio/alida/index.php/Projects here].</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Main_Page&diff=306Main Page2017-03-28T08:25:06Z<p>Moeller: /* Alida - Advanced Library for Integrated Development of Data Analysis Applications */</p>
<hr />
<div>== Alida - <span style="color:#CC0000">A</span>dvanced <span style="color:#CC0000">L</span>ibrary for <span style="color:#CC0000">I</span>ntegrated <span style="color:#CC0000">D</span>evelopment of Data Analysis <span style="color:#CC0000">A</span>pplications ==<br />
<br />
...formerly known as Alida - <span style="color:#CC0000">A</span>utomatic <span style="color:#CC0000">L</span>ogging of Process <span style="color:#CC0000">I</span>nformation in <span style="color:#CC0000">D</span>ata <span style="color:#CC0000">A</span>nalysis <br />
<br />
{|width="100%"<br />
|-<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''What is Alida?'''<br><br />
Alida defines a concept for designing libraries and toolkits in data analysis. It supports and simplifies integrated algorithm development by inherently joining algorithm implementation, automatic analysis process documentation and fully generic generation of user interfaces. In Alida each data analysis or manipulation action is realized in terms of an operator that acts on given data to produce desired output data. As all operators implement a common interface definition, their input and output parameters are accessible in a standardized manner, and they can also be invoked in a predefined way. Alida's concept is well-suited to ease algorithm development and their application to real-world problems by non-expert users. Due to the operator interface definition and the unified handling of operators it is for example possible to automatically generate user interfaces for operators, i.e. graphical frontends or commandline interfaces.<br />
<br />
The Alida concept is independent of a specific programming language, however, relies on an object-oriented design. Moreover, in particular Java renders it quite easy to implement the conceptual features of Alida due to its reflection and annotation mechanisms. Consequently currently there is only active maintenance and support for the Java implementation of the concept. A prototypical C++ implementation is also available [[CPlusPlus | (C++ version)]], however, still lacks a lot of features and is in general at a rather early stage.<br />
<br />
The Java implementation of the Alida concept is in a quite mature state. It provides a framework for implementing and running operators. It also includes automatic process documentation and automatically generated command line and graphical user interfaces. Calls to operators not only produce data analysis results, but are at the same time registered within the framework together with all input and output objects as well as parameters settings of the various operators. These data acquired during an analysis process and the order of operator calls form a directed graph datastructure containing all relevant information for later reconstruction or verification of the analysis procedure. <br />
The Java implementation of Alida allows to make the directed graph datastructure explicit in terms of XML representations which can be visually explored with appropriate graphical frontends like Chipory, or might be stored in data bases for archival purposes.<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Grappa - the Graphical Programming Editor for Alida'''<br><br />
<br />
[[file:Grappa_logo.png|left|link=]] <br />
Since release 2.0 Alida extends its operator concept towards combining operators into more complex workflows. A workflow is defined as a combination of operators being excuted sequentially, in parallel or in a nested fashion.<br> The design of such workflows can best be done graphically, and consequently the Java implementation of Alida now includes '''''Grappa''''', a graphical programming editor for designing workflows. Grappa provides users with an intuitive tool for developing sophisticated image analysis workflows.<br />
All Alida operators are right away available as operator nodes in Grappa and form the building blocks for workflows.<br><br />
</div><br />
</div><br />
|<br />
|style="vertical-align:top" |<br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''How to get Alida?'''<br><br />
* You can download Alida 2.7.3 [[Downloads | here]]. <br/> <br />
<br />
* You can find the API documentation for this release [http://www2.informatik.uni-halle.de/agprbio/alida/api/java/index.html here].<br/> <br />
<br />
* Alida offers you a user and programmer guide which you can download [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf here].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Latest News'''<br><br />
* 03/2017: A new article about Alida entitled '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''' has just been published in the ''Journal of Open Research Software'', 5(1):7, 2017, DOI:[http://doi.org/10.5334/jors.124]. <br />
* 03/2016: Alida 2.7 has been released.<br>Note that Alida from now on requires '''''Java 8'''''.<br>The release is also available from [http://dx.doi.org/10.5281/zenodo.47586 Zenodo] and from our Maven repository server [https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida/2.7 moon]<br />
The news archive can be found [[NewsArchive | here]].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Licensing information'''<br><br />
Alida is free software: you can redistribute it and/or modify under the terms of the [http://www.gnu.org/licenses/gpl-3.0.html GNU General Public License version 3] or (at your option) any later version as published by the [http://www.fsf.org/ Free Software Foundation].<br />
</div><br />
</div><br />
<br><br />
<div style="margin: 0; margin-right:10px; border: 2px solid #dfdfdf; background-color:#f8f8ff;"><br />
<div style="padding: 0.3em 1em 0.7em 1em;"><br />
'''Bug reports & Feature requests'''<br><br />
Bug reports and feature requests can be submitted as issues on [https://github.com/alida-hub/alida/issues Github]. Before reporting a new bug, please check if that bug has already been submitted.<br />
</div><br />
</div><br />
|}</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=NewsArchive&diff=305NewsArchive2017-03-28T08:24:49Z<p>Moeller: </p>
<hr />
<div>== News Archive ==<br />
<br />
* 06/2015: Alida's sources are now available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida]<br />
<br />
* 06/2015: Alida 2.6 has been released.<br />
<br />
* 03/30/2015: <br>Release of version 2.5.<br> Alida now supports callback functions attached to parameters which are called upon changes of the values of the parameters. This, e.g., allows for dynamic updates of the set of parameters of an operator and for dynamic configuration of the GUI.<br />
<br />
* 01/07/2015: <br>Release of version 2.4.4.<br />
<br />
* 12/04/2014: <br>Alida and in particular its technical ingredients will be presented at the '''OGRW 2014''', which is the 9th Open German-Russian Workshop on Pattern Recognition and Image Understanding.<br> The title of the contribution is '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms'''''.<br> The workshop is taking place this week in Koblenz/Germany.<br />
<br />
* 12/01/2014: <br>Release of version 2.4.3.<br />
<br />
* 07/25/2014: <br>Release of version 2.4.2<br> Some more bugfixes.<br />
<br />
* 07/18/2014: <br>Release of version 2.4.1<br> Bugfixed an annoying problem with keyboard shortcuts.<br />
<br />
* 06/29/2014: <br>Release of version 2.4.<br> Main new feature is the support for progress events of operators. In addition, numerous bugfixes and enhancements in the graphical user interfaces are included.<br />
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* 01/31/2014: <br>Release of version 2.3.1.<br> A serious bug in saving and loading workflows and operator configurations was fixed.<br />
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* 01/17/2014: <br>Release of version 2.3.<br> The project management of the Alida Java project has switched to Maven, i.e. from now on Alida can be downloaded directly from our Maven server.<br> The new release by itself mainly includes bugfixes in the core of Alida improving the stability. <br />
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* 05/17/2013: <br> Alida will be presented at the '''MVA 2013''', which is the Thirteenth IAPR International Conference on Machine Vision Applications.<br> The title of the contribution is '''''A Framework Unifying the Development of Image Analysis Algorithms and Associated User Interfaces'''''.<br> The conference will take place in Kyoto/Japan from May 21st to 23rd. We hope to meet you there!<br />
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* 05/17/2013: <br>Release of version 2.2.<br> Grappa has increased its user-friendliness by supporting key shortcuts now. In addition, the mechanism to save and load configurations in Alida<br> has switched from the Java serialization framework to XML beans. Finally, many bugfixes in Alida's core were again applied.<br />
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* 02/28/2013: <br>Release of version 2.1.<br> The new release includes many bugfixes in Alida's core improving the stability, and minor improvements regarding layout and handling of Alida's user interfaces.<br> Note that also a new version of the manual was released which now covers all important aspects of programming with Alida.<br />
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* 12/20/2012: <br>Release of version 2.0.<br> This version includes the graphical editor '''Grappa''' to compose workflows of operators.<br />
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* 11/10/2012: <br> Updated version of Chipory available for download.<br />
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* 26/07/2012: <br> Alida will be presented at the '''''ImageJ User & Developer Conference 2012''''' to be held at the end of October in Mondorf-les-Bains, Luxembourg.<br> There will be a poster presentation combined with a demo entitled [http://imagejconf.tudor.lu/program/poster/birgit_moeller996310491 '''Automatic Generation of Processing Histories using Alida'''].<br> It will provide an introduction to the processing history mechanism implemented in Alida, and its usage.<br> Also a talk will be given about our new graphical editor ''Grappa'' entitled '''Graphical Programming in Alida and ImageJ 2.0 with Grappa'''.<br />
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* 12/07/2012: <br>New release of chipory ready for download<br />
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* 21/03/2012:<br> Alida will be presented at the '''''IEEE International Symposium on Biomedical Imaging (ISBI)''''' to be held at the end of April in Barcelona.<br> There will be a poster presentation combined with a demo at the '''''Bioimage Analysis Workshop on Open Source Software''''' held in conjunction with ISBI.<br> The title will be '''ALIDA - Automatic generation of user interfaces for data analysis algorithms'''.<br />
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* 12/03/2012:<br> The Alida concept now features a prototypical implementation in C++! It supports generic operator execution from command line.<br>Release 0.1 is available now from the download page.<br />
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* 02/03/2012:<br>Alida release 1.2 has just been published! You can get the new version in the download section!<br>Main new feature: generic user interface generation for operators to use them from commandline and via a Swing GUI!</div>Moellerhttps://alida.informatik.uni-halle.de/index.php?title=Projects&diff=304Projects2017-03-28T08:09:15Z<p>Moeller: </p>
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<div>== Related Projects ==<br />
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* '''''MiToBo - A microscope image analysis toolbox'''''<br>Webpage: [http://www.informatik.uni-halle.de/mitobo http://www.informatik.uni-halle.de/mitobo]<br />
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== Publications ==<br />
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* S. Posch and B. Möller, '''''Alida - Advanced Library for Integrated Development of Data Analysis Applications''''',<br> Journal of Open Research Software, 5(1):7, DOI: http://doi.org/10.5334/jors.124, 2017.<br />
* S. Posch and B. Möller, '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms''''',<br> Pattern Recognition and Image Analysis, ISSN 1054-6618, Vol. 26, No. 1, pp. 181-189, 2016.<br />
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* S. Posch and B. Möller, '''''Design and Implementation of the Alida Framework to Ease the Development of Image Analysis Algorithms''''',<br> 9th Open German-Russian Workshop on Pattern Recognition and Image Understanding (OGRW), Electronic on-site Proceedings, Koblenz, Germany, December 2014.<br />
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* B. Möller and S. Posch, '''''A Framework Unifying the Development of Image Analysis Algorithms and Associated User Interfaces''''',<br> In Proc. of 13th IAPR International Conference on Machine Vision Applications (MVA '13), pp. 447-450, Kyoto, Japan, May 2013.<br />
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* S. Kirchner, S. Posch and B. Möller, '''''Graphical Programming in Alida and ImageJ 2.0 with Grappa''''',<br> In Proc. of ImageJ User & Developer Conference, pp. 138-143, ISBN 2-919941-18-6, Mondorf-les-Bains, Luxembourg, October 2012. <br />
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* S. Posch and B. Möller, '''''Automatic Generation of Processing Histories using Alida''''',<br> In Proc. of ImageJ User & Developer Conference, pp. 218-221, ISBN 2-919941-18-6, Mondorf-les-Bains, Luxembourg, October 2012.<br> This contribution was awarded as the "Best Scientific Poster" of the ImageJ conference!<br />
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* S. Posch and B. Möller, '''''Alida - Automatic Generation of User Interfaces for Data Analysis Algorithms''''',<br> Poster presentation at IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI), Bioimage Analysis Workshop , Barcelona, Spain, April 2012.<br />
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* B. Möller, O. Greß and S. Posch, '''''Knowing what happened - Automatic Documentation of Image Analysis Processes''''',<br> In Proc. of 8th International Conference on Computer Vision Systems (ICVS '11), J.L. Crowley, B.A. Draper, and M. Thonnat (Eds.),<br> Springer, LNCS 6962, pp. 1-10. Inria Sophia Antipolis, France, September 2011.</div>Moeller