About

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 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.

Contact

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

Project coordinators:
Alexander Mazein alexander.mazein@uni.lu
Irina Balaur irinaa.balaur@gmail.com

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.

Project team





Irina Balaur

European Institute for Systems Biology and Medicine, Lyon, France

Alexander Mazein

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg

Charles Auffray

European Institute for Systems Biology and Medicine, Lyon, France

Antonio Fabregat

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK





Adrien Rougny

National Institute of Advanced Industrial Science and Technology, Tokyo, Japan

Vasundra Touré

Norwegian University of Science and Technology (NTNU), Trondheim, Norway

Hanna Borlinghaus

University of Konstanz, Konstanz, Germany

Falk Schreiber

University of Konstanz, Konstanz, Germany





Olga Ivanova

Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands

James Greene

University of Connecticut School of Medicine, Farmington, USA

Michael Blinov

University of Connecticut School of Medicine, Farmington, USA

Tatiana Serebriiskaia

Moscow Institute of Physics and Technology, Moscow, Russia





Valeriya Berzhitskaya

Moscow Institute of Physics and Technology, Moscow, Russia

Maria Kondratova

Computational Systems Biology of Cancer, Institut Curie, Paris, France

Inna Kuperstein

Computational Systems Biology of Cancer, Institut Curie, Paris, France

Matthias König

Systems Medicine of the Liver, Humboldt University of Berlin, Germany





Marek Ostaszewski

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg

Reinhard Schneider

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg

Maria del Carmen
Heredia

University of Connecticut, Storrs, USA

John Albanese

Trinity College, Hartford, USA


Collaborative network