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README.md

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Project

The aim is to provide the most accurate translation possible between CellDesigner and SBGN-ML file formats. Translation in both direction is possible. A webservice using this library can be found here with a sample usage in Newt. This project should ultimately be integrated into SBFC.

Compatible formats:

  • SBML Level 2 Version 4, CellDesigner modelVersion 4.0 (output of CellDesigner 4.4)
  • SBGN-ML 0.2 (PD)

To download the full app directly, go to the release page.

More information can be found in the Wiki.

Javadoc is available here.

All known issues and limitations of the translator are listed in the issues and on this wiki page.

Requirements

  • Java 8 (with JavaFX if you want to use the GUI)
  • Maven (tested with Maven 3.5)

Install

After cloning the repository and getting into its directory:

mvn clean

mvn install

This will output 2 jars in the target/ directory:

  • cd2sbgnml-{version}.jar: the bare compiled project, with no dependency included. Can be used directly in other Java projects.
  • cd2sbgnml-{version}-app.jar: the full project with all dependencies included. Scripts and GUI provided here can be used.

Javadoc can be generated with:

mvn javadoc:javadoc

Usage

After install, you can use the 2 bash scripts to run a conversion from command line (from the project's root directory):

cd2sbgnml.sh <input file> <output file>

sbgnml2cd.sh <input file> <output file>

A small GUI is also provided as the main class of the package. It can be launched by double clicking on the jar or by directly calling the package with java -jar. Be sure to have JavaFX working in your Java distribution.

With the scripts, all log messages will go to System.out. With the GUI, everything will be written in the selected log file.

Translation of large-scale biological maps - examples:

Contributions and issues

If you have any suggestions or want to report a bug, don't hesitate to create an issue. Pull requests and all forms of contribution will be warmly welcomed.

Useful links

Acknowledgements

This work was initially done by Ludovic Roy at SysBio group, Institut Curie, under the supervision of Andrei Zinovyev in collaboration with Alexander Mazein from EISBM. The work was initiated in connection to the efforts of the Disease Maps and SBGN communities.

Thanks to Frank T. Bergmann for his SBGN rendering tool which made debugging a whole lot easier.

Thanks to Nicolas, Laetitia, Henri, Choumouss and Julien for the everyday office mate support.

And thanks to Olga Ivanova for this translation rule sheet that, in the end, definitely had a real part in this project.

This work has received funding from the European Union Horizon 2020 research and innovation programme under grant agreement No 668858.