1. Standards and formats in systems biology
Eric Bonnet
Computational Systems Biology of Cancer
Institut Curie - INSERM U900 - Mines ParisTech
Seminar Mathematics and Biology of Cancer
Institut Curie 12/06/2013 1

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er tumor

5. Pathway databases

7. Why do we need standards?
Evil.
Yes, we can.

8. Systems Biology standard formats
Open access.
Dynamic, community-driven development.
Promote development and use of software libraries.
SBML Community organization
SBML Forum (propositions)
SBML Editors (evaluation, reconciliation)
SBML Team (funding, material)
SBML SAB (guidance)

12. BiNoM Structure analysis BiNoM BioPAX Utilities
BiNoM, a Biological Network Manager
BiNoM Utilities
BiNoM Structure analysis
BiNoM BioPAX Query
BiNoM I/O
BiNoM BioPAX Utilities
BiNoM Modules
Cytoscape plugin.
Supports standard systems biology formats (BioPAX, CellDesigner, etc.).
Facilitates the visualization and manipulation of biological networks.
Help the user to analyze, extract and condense network information.

13. Modular representation
Cell Cycle regulation RB / E2F network, 70+ proteins, 150+ genes, 200 species, 160+ reactions
Modular representation
Graph pruning, extracting strongly connected components, decomposition into cycles, finding shortest, subpotimal, all paths, clustering subgraphs, export to SBML

15. Acknowledgements
Laurence Calzone Daniel Rovera Gautier Stoll Paola Vera-Licona Emmanuel Barillot Eric Viara Andrei Zinovyev