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, the United States, Russia 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). There is a list of selected topics that are already in work or being prepared for curation.
In additon to GraphML and SBGN-ML, we aim to provide maps in various formats including CellDesigner, SBML and BioPAX, so the models are easily accessible and can be downloaded, reused and improved. These formats will be generated automatically.
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, the main tool in this project. Resulting format: GraphML. Please review tips on how to draw SBGN diagrams in yEd. Also, any tool that generates valid SBGN-ML can be used, for example SBGN-ED or Newt Editor, and in that case the files are to be provided in SBGN-ML.
- Proposing new topics: it can be done through direct search on the subject of metabolism regulation or by working with the automatically assembled lists.
- Proposing new colour schemes. We are looking for ways to improve the diagrams aestetically. To experiment with colours and layouts, download any diagram in GraphML format and edit as you prefer.
To join the effort please use this email address:
Alexander Mazein, Irina Balaur, Antonio Fabregat, Hanna Borlinghaus, Falk Schreiber, Valeriya Berzhitskaya, Tatiana Serebriiskaia, Adrien Rougny, Vasundra Toure, Olga Ivanova, James Greene, John Albanese, Maria del Carmen Heredia, Michael Blinov, Maria Kondratova, Inna Kuperstein, Marek Ostaszewski, Piotr Gawron, Frank Bergmann, Hong-Wu Ma, Igor Goryanin, Ines Thiele, Charles Auffray, Reinhard Schneider
|Alexander Mazein||Irina Balaur
Senior Software Engineer
|Vasundra Toure||Hanna Borlinghaus|
|Falk Schreiber||Valeriya Berzhitskaya|
|Tatiana Serebriiskaia||James Greene|
|Maria del Carmen Heredia||John Albanese|
|Michael Blinov||Olga Ivanova
Member of Scientific Staff
Henrik Kacser Chair in Systems Biology
Professor in Systems Biomedicine
Research Director at CNRS
Head of Bioinformatics Core Facility