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Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech

BiNoM 2.0, a versatile tool for accessing and analyzing pathways using standard systems biology formats. Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech http://sysbio.curie.fr Workshop NUS-IBENS 30/05/2013. Pathway databases.

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Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech

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  1. BiNoM 2.0, a versatile tool for accessing and analyzing pathways using standard systems biology formats Eric Bonnet Computational Systems Biology of Cancer Institut Curie - INSERM U900 - Mines ParisTech http://sysbio.curie.fr Workshop NUS-IBENS 30/05/2013

  2. Pathway databases

  3. Molecular reactions maps RB / E2F map

  4. Standard formats

  5. BiNoM, a Biological Network Manager BiNoM Modules BiNoM Structure analysis BiNoM I/O BiNoM Utilities BiNoM BioPAXUtilities BiNoM BioPAX Query • 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.

  6. BiNoM Use of data from public pathway databases for modelling purposes (from Bauer-Mehren et al., Pathway databases and tools for their exploitatation: benefits, current limitations and challenges. 2009 Molecular Systems Biology 5:290).

  7. Modular representation RB / E2F network, 70+ proteins, 160+ reactions, 350 publications Modularrepresentation

  8. Non-invasive cancers Invasive cancers

  9. OCSANA: Optimal Combinations of Interventions for Network Analysis • Influence graph G. • Input nodes I1, I2. • Output (target) node O1. I1 -> B -> C -> O1 I1 -> E -> C -> O1 I2 -> E -> C -> O1 • Combinations of Interventions: {C}, {E, B}, {I1, I2} • Application of OCSANA: candidate drugtargetsdiscovery.

  10. OCSANA CI search algorithms • Finding CIs is a combinatorial problem. • Berge’s algorithm (1989) • Recursive calculation of transervals on a hypergraph. • Exact and complete, but do not scale well for networks 50+ nodes. • Approximation solution. • Use a score to reduce the search space. • Score is based on the network structure.

  11. BiNoM Team • Laurence Calzone • Daniel Rovera • Gautier Stoll • Paola Vera-Licona • Emmanuel Barillot • Andrei Zinovyev • http://binom.curie.fr • http://apps.cytoscape.org/apps/binom

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