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, 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.

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, 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

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
Moscow Institute of Physics and Technology, Moscow, Russia
Contribution: Cholesterol, Glycogen, cAMP hydrolysis, Acyl-carnitine, Triacylglycerol

Tatiana Serebriiskaia

Senior Researcher
Moscow Institute of Physics and Technology, Moscow, Russia
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

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

Marek Ostaszewski

Research Scientist
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
Contribution: MINERVA support, SBGN-ML import/export support in MINERVA

Hong-Wu Ma

Professor
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
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


Collaborative network