The project was initiated by the European Institute for Systems Biology and Medicine (EISBM) in collaboration with the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). The project team includes participants with expertise in systems biomedicine, computational biology, pathway curation and standard formats from research groups in France, the United Kingdom, Luxembourg, Norway, the Netherlands, Germany, Belgium, the United States, China and Japan.

How to contribute

To learn more and to contribute, please review the available maps, a collection of diagrams in Systems Biology Graphical Notation (SBGN).

In addition to GraphML and SBGN-ML, we aim to provide maps in various formats including CellDesigner, SBML and BioPAX, so the maps are easily accessible and can be downloaded, reused and improved. Maps are currently available in GraphML, SBGN-ML, CellDesigner and SBML.

Ways to contribute:

• Drawing diagrams: please join the work on one of the existing topics or propose a new one. Diagrams can be drawn using the SBGN palette in the yEd Graph Editor, one of the main tools used in this project. The resulting format is GraphML. Please review tips on how to draw SBGN diagrams in yEd. Any tool that generates valid SBGN-ML can also be used, for example SBGN-ED or Newt Editor, in which case the files are to be provided in SBGN-ML.
• Proposing new topics: this can be done by searching the literature on metabolism regulation or by working with the automatically assembled lists.
• Proposing new colour schemes. We are looking for ways to improve the diagrams aesthetically. To experiment with colours and layouts, download any diagram in GraphML format and edit it as you prefer.

License

The map diagrams and the corresponding data files are distributed under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0).

Contact

To join the effort, please use this email address:
metabolismregulation@googlegroups.com

Project coordinators:
Alexander Mazein a.mazein@gmail.com
Irina Balaur irina.a.balaur@gmail.com