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= Java | ==== Current Java release ==== | ||
The current release of Alida is 3.0.2. | |||
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: | |||
[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] | |||
For download the following files are of interest: | |||
* Distribution: the complete Alida Distribution including all dependencies and documentation (zip format) | |||
* Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here) | |||
* API: the Alida Javadoc API (jar format)<br> | |||
Alida's source code is also available from Github: [https://github.com/alida-hub/alida https://github.com/alida-hub/alida] | |||
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.<br> | |||
==== Long-term archival of major releases ==== | |||
Major releases of Alida are archived at [https://zenodo.org/ Zenodo] including a persistent DOI for citations: | |||
* [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> | |||
* [https://zenodo.org/record/47586 Alida 2.7], [[Image:zenodo.47586.svg.png|150px|link=https://doi.org/10.5281/zenodo.47586]]<br> | |||
==== Using Alida in your own code ==== | ==== Using Alida in your own code ==== | ||
Line 49: | Line 25: | ||
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: | 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: | ||
* Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven | * Maven-Template Project: [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/alida-project-template-maven-src.zip zip] | ||
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. | 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> | ||
= Manual = | ==== Manual ==== | ||
Detailed information about Alida, its API and usage, can be found in the user and programmer manual. | Detailed information about Alida, its API and usage, can be found in the user and programmer manual. | ||
* Alida-Manual, Version 2 | * Alida-Manual, Version 3.0.2 [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/manual/AlidaManual.pdf pdf] (April 2021) | ||
<br/> | <br/> | ||
= Additional resources = | ==== Additional resources ==== | ||
* '''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. | * '''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. | ||
Line 76: | Line 52: | ||
<br/> | <br/> | ||
==== Logos ==== | |||
= Logos = | |||
* Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF] | * Alida logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Alida_logo.pdf PDF] | ||
* Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF] | * Grappa logo as [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/Grappa_logo.pdf PDF] | ||
<br> | |||
==== Release Archive (>= 2.3) ==== | |||
{| border = "1" cellpadding = "5pt" cellspacing = "0" style = "border-color: #DDD; text-align: center; width: 80%" | |||
! Version | |||
! Distribution | |||
! Binaries only | |||
! API | |||
! Date | |||
|- | |||
| 3.0 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/3.0/alida-3.0-javadoc.jar jar] | |||
| May 15th, 2020 | |||
|- | |||
| 2.7.13 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.13/alida-2.7.13-javadoc.jar jar] | |||
| February 20th, 2020 | |||
|- | |||
| 2.7.12 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.12/alida-2.7.12-javadoc.jar jar] | |||
| September 12th, 2019 | |||
|- | |||
| 2.7.11 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.11/alida-2.7.11-javadoc.jar jar] | |||
| July 25th, 2019 | |||
|- | |||
| 2.7.10 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.10/alida-2.7.10-javadoc.jar jar] | |||
| February 11th, 2019 | |||
|- | |||
| 2.7.9 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.9/alida-2.7.9-javadoc.jar jar] | |||
| December 12th, 2018 | |||
|- | |||
| 2.7.8 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.8/alida-2.7.8-javadoc.jar jar] | |||
| September 3rd, 2018 | |||
|- | |||
| 2.7.7 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.7/alida-2.7.7-javadoc.jar jar] | |||
| May 18th, 2018 | |||
|- | |||
| 2.7.6 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.6/alida-2.7.6-javadoc.jar jar] | |||
| March 23rd, 2018 | |||
|- | |||
| 2.7.5 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.5/alida-2.7.5-javadoc.jar jar] | |||
| November 10th, 2017 | |||
|- | |||
| 2.7.4 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.4/alida-2.7.4-javadoc.jar jar] | |||
| July 29th, 2017 | |||
|- | |||
| 2.7.3 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.3/alida-2.7.3-javadoc.jar jar] | |||
| December 12th, 2016 | |||
|- | |||
| 2.7.2 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.2/alida-2.7.2-javadoc.jar jar] | |||
| May 20th, 2016 | |||
|- | |||
| 2.7.1 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7.1/alida-2.7.1-javadoc.jar jar] | |||
| May 20th, 2016 | |||
|- | |||
| 2.7 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.7/alida-2.7-javadoc.jar jar] | |||
| March 15th, 2016 | |||
|- | |||
| 2.6 | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-bin.zip zip] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6.jar jar] | |||
| [https://moon.informatik.uni-halle.de/archiva/repository/releases/de/unihalle/informatik/Alida/alida/2.6/alida-2.6-javadoc.jar jar] | |||
| June 17th, 2015 | |||
|- | |||
| 2.5 | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-bin.zip zip] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5.jar jar] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.5-javadoc.jar jar] | |||
| March 30th, 2015 (Callbacks) | |||
|- | |||
| 2.4.4 | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-bin.zip zip] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4.jar jar] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.4-javadoc.jar jar] | |||
| Jan 7th, 2015 | |||
|- | |||
| 2.4.3 | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-bin.zip zip] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3.jar jar] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.3-javadoc.jar jar] | |||
| Dec 1st, 2014 | |||
|- | |||
| 2.4.2 | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-bin.zip zip] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2.jar jar] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.2-javadoc.jar jar] | |||
| Jul 25th, 2014 | |||
|- | |||
| 2.4.1 | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-bin.zip zip] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1.jar jar] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.1-javadoc.jar jar] | |||
| Jul 18th, 2014 | |||
|- | |||
| 2.4 | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-bin.zip zip] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4.jar jar] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.4-javadoc.jar jar] | |||
| Jun 29th, 2014 | |||
|- | |||
| 2.3.1 | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-bin.zip zip] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1.jar jar] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.1-javadoc.jar jar] | |||
| Jan 31st, 2014 | |||
|- | |||
| 2.3 | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-bin.zip zip] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3.jar jar] | |||
| [http://www2.informatik.uni-halle.de/agprbio/alida/downloads/java/Alida-2.3-javadoc.jar jar] | |||
| Jan 16th, 2014 | |||
|} | |||
<br> | |||
= | ==== Release Archive (< 2.3) ==== | ||
== | |||
= | |||
In the pre-Maven era Alida's dependencies on external jars had to be managed manually. | In the pre-Maven era Alida's dependencies on external jars had to be managed manually. | ||
Alida required some external jars included in the Alida binary zipfiles (since v2.0). | Alida required some external jars included in the Alida binary zipfiles (since v2.0). | ||
Line 176: | Line 284: | ||
<br/> | <br/> | ||
==== Alida in C++ ==== | |||
== C++ | 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 |
Latest revision as of 09:59, 9 April 2021
Current Java release
The current release of Alida is 3.0.2.
Since release 2.3 we support Maven for managing Alida's project resources.
You can download Alida following the links below in the table and also as Maven artifacts from our Maven server:
https://moon.informatik.uni-halle.de/archiva/#artifact/de.unihalle.informatik.Alida/alida
For download the following files are of interest:
- Distribution: the complete Alida Distribution including all dependencies and documentation (zip format)
- Binaries only: the Alida binaries only, mainly suitable for development purposes (note that dependencies are not included here)
- API: the Alida Javadoc API (jar format)
Alida's source code is also available from Github: https://github.com/alida-hub/alida
Note that since version 2.7 Alida's implementation strictly requires Java 1.8.
Long-term archival of major releases
Major releases of Alida are archived at Zenodo including a persistent DOI for citations:
Using Alida in your own code
For using Alida as a library in your own code the most easy way to fulfill all requirements and dependencies is to use Maven.
Since Alida version 2.4 we offer a template Maven project which you can use as a starting point for your work:
- Maven-Template Project: zip
Just unzip the archive to a directory of your choice and follow the instructions in the README file included.
The project already defines all repositories and dependencies required to use Alida's functionality.
Manual
Detailed information about Alida, its API and usage, can be found in the user and programmer manual.
- Alida-Manual, Version 3.0.2 pdf (April 2021)
Additional resources
- Chipory - a graph visualization tool for displaying MiToBo history graphs
Chipory is an extended version of the Chisio software developed at the Bilkent University in Turkey.
The zip file below contains all necessary files. Download this file and unpack it into a folder of your choice.
- To use Chipory on a Linux system with 32-bit architecture just type './Chipory.sh'.
- In case that your machine has a 64-bit architecture running Linux, call './Chipory_64.sh'.
- For Windows with 32-bit architecture a self extracting installer including an executable of Chipory is available.
Download the current release as of 7-12-2012:
- Chipory binary zip
- self extracting installer for Windows chipory-setup.exe
Source code for Chipory is available upon request.
Logos
Release Archive (>= 2.3)
Version | Distribution | Binaries only | API | Date |
---|---|---|---|---|
3.0 | zip | jar | jar | May 15th, 2020 |
2.7.13 | zip | jar | jar | February 20th, 2020 |
2.7.12 | zip | jar | jar | September 12th, 2019 |
2.7.11 | zip | jar | jar | July 25th, 2019 |
2.7.10 | zip | jar | jar | February 11th, 2019 |
2.7.9 | zip | jar | jar | December 12th, 2018 |
2.7.8 | zip | jar | jar | September 3rd, 2018 |
2.7.7 | zip | jar | jar | May 18th, 2018 |
2.7.6 | zip | jar | jar | March 23rd, 2018 |
2.7.5 | zip | jar | jar | November 10th, 2017 |
2.7.4 | zip | jar | jar | July 29th, 2017 |
2.7.3 | zip | jar | jar | December 12th, 2016 |
2.7.2 | zip | jar | jar | May 20th, 2016 |
2.7.1 | zip | jar | jar | May 20th, 2016 |
2.7 | zip | jar | jar | March 15th, 2016 |
2.6 | zip | jar | jar | June 17th, 2015 |
2.5 | zip | jar | jar | March 30th, 2015 (Callbacks) |
2.4.4 | zip | jar | jar | Jan 7th, 2015 |
2.4.3 | zip | jar | jar | Dec 1st, 2014 |
2.4.2 | zip | jar | jar | Jul 25th, 2014 |
2.4.1 | zip | jar | jar | Jul 18th, 2014 |
2.4 | zip | jar | jar | Jun 29th, 2014 |
2.3.1 | zip | jar | jar | Jan 31st, 2014 |
2.3 | zip | jar | jar | Jan 16th, 2014 |
Release Archive (< 2.3)
In the pre-Maven era Alida's dependencies on external jars had to be managed manually. Alida required some external jars included in the Alida binary zipfiles (since v2.0).
For earlier versions the following external jars are needed to use Alida:
In addition, Alida requires some more libraries which are in-house developments:
- Alida requires some graphml extensions to be found in aldgraphml.jar.
- 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.
- The graphical operator runner features an online help system based on JavaHelp System which is included in Alida-Help.jar.
If you download the Alida binary zipfile you will find these two libraries in the subdirectory intjars of the zipfile.
Make sure that all of them are in the classpath when executing the operator runners.
Version | Binaries | Sources | API | Date |
---|---|---|---|---|
2.2.1 | zip | zip | zip | May 17th, 2013 (Bugfix Release) |
2.2 | zip | zip | zip | May 17th, 2013 |
2.1 | zip | zip | zip | February 28th, 2013 |
2.0 | zip | zip | zip | December 20th, 2012 |
1.2 | zip | zip | zip | March 2nd, 2012 |
1.1 | zip | zip | zip | Sep 14th, 2011 |
1.0 | zip | zip | zip | May 9th, 2011 |
Alida in C++
Alida's concept is implemented in Java and prototypically in C++ (the implementation can be found 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.