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 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). 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.

License

The map diagrams and the corresponding data files are distributed under the terms of the Creative Commons Public Domain (CC0) License.

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

Project team

Alexander Mazein, Irina Balaur, Antonio Fabregat, Hanna Borlinghaus, Falk Schreiber, Valeriya Berzhitskaya, Tatiana Serebriiskaia, Adrien Rougny, Vasundra Toure, Olga Ivanova, Marcio Luis Acencio, Michael Blinov, Luiz Ladeira, Alexander Kuritsyn, James Greene, John Albanese, Maria del Carmen Heredia, Ahmed Hemedan, Marek Ostaszewski, Piotr Gawron, Frank Bergmann, Anatoly Sorokin, Hong-Wu Ma, Nikolaus Berndt, Venkata Satagopam, Igor Goryanin, Ines Thiele, Charles Auffray, Reinhard Schneider

	Alexander Mazein Researcher Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg Contribution: Project coordination, Glycolysis, Glycogen, Mevalonate, iNOS, Aspirin		Irina Balaur Postdoctoral researcher Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg Contribution: Project coordination, Recon2Neo4j, Reactome-Recon lists
	Antonio Fabregat Senior Software Engineer European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK Contribution: Reactome Neo4j, Reactome-Recon lists		Adrien Rougny Researcher National Institute of Advanced Industrial Science and Technology, Tokyo, Japan Contibution: Acetyl-CoA
	Vasundra Toure PhD Student Department of Biology Norwegian University of Science and Technology, Trondheim, Norway Contribution: Glycolysis, Glycogen		Hanna Borlinghaus PhD Student University of Konstanz, Konstanz, Germany Contribution: Estradiol, Pyrimidine, Glutaminolysis
	Falk Schreiber Chair for Life Science Informatics University of Konstanz, Konstanz, Germany Contribution: Resources, Estradiol, Pyrimidine, Glutaminolysis		Valeriya Berzhitskaya Researcher Systems Biology and Translational Medicine, EPAM Systems, Inc., Newtown, USA Contribution: Cholesterol, Glycogen, cAMP hydrolysis, Acyl-carnitine, Triacylglycerol
	Tatiana Serebriiskaia Director Systems Biology and Translational Medicine, EPAM Systems, Inc., Newtown, USA Contribution: Resources, Cholesterol, Glycogen, cAMP hydrolysis, Acyl-carnitine, Triacylglycerol		James Greene MSc Student University of Connecticut School of Medicine, Farmington, USA Contribution: Mevalonate, Phosphoinositides
	Maria del Carmen Heredia MSc Student University of Connecticut, Storrs, USA Contribution: Annotation, Glycolysis, Eicosanoids, Cholesterol, iNOS, Acyl-carnitine, Glutaminolysis, Aspirin		John Albanese MSc Student Trinity College, Hartford, USA Contribution: Annotation, Glycogen, Glycogen, Acetyl-CoA, eNOS, cAMP, Triacylglycerol, Estradiol, Pyrimidine
	Michael Blinov Assistant Professor University of Connecticut School of Medicine, Farmington, USA Contribution: Resources, Mevalonate, Phosphoinositides		Olga Ivanova Junior Researcher Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands Contribution: eNOS
	Luiz Ladeira Postdoctoral Researcher GIGA In Silico Medicine, University of Liège, Liège, Belgium Contribution: Annotation, Glycogen		Alexander Kuritsyn Independent Researcher Tbilisi, Georgia Contribution: Annotation
	Frank Bergmann Member of Scientific Staff University of Heidelberg, Heidelberg, Germany Contribution: SBGN-ML 0.3 support		Piotr Gawron Researcher Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg Contribution: MINERVA support, SBGN-ML import/export support in MINERVA
	Marcio Luis Acencio Researcher Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg Contribution: Citrullination		Ahmed Hemedan Researcher Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg Contribution: Computational modelling
	Marek Ostaszewski Research Scientist Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg Contribution: MINERVA support, SBGN-ML import/export support in MINERVA		Venkata Satagopam Deputy Head of Bioinformatics Core Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg Contribution: Support at the LCSB, MINERVA support
	Nikolaus Berndt Group Leader, Metabolic and Biophysical Simulations in Systems Medicine Charité Universitätsmedizin Berlin, Germany Contribution: Glycogen metabolism example, modelling		Hong-Wu Ma Professor Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China Contribution: Initial discussion, concept development, Recon2 project
	Anatoly Sorokin Senior Computational Biologist Okinawa Institute of Science and Technology, Tancha, Japan Contribution: Initial discussion, concept development, Recon2 project		Igor Goryanin Henrik Kacser Chair in Systems Biology School of Informatics, University of Edinburgh, Edinburgh, UK Contribution: Initial discussion, concept development, Recon2 project
	Ines Thiele Professor in Systems Biomedicine National University of Ireland Galway (NUI Galway), Galway, Ireland Contribution: Project planning, Recon2 project		Charles Auffray Research Director at CNRS Founding Director of the EISBM European Institute for Systems Biology and Medicine, Lyon, France Contribution: Support at the EISBM
	Reinhard Schneider Head of Bioinformatics Core Facility Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg Contribution: Support at the LCSB, MINERVA support