BiNoM 2.0, a versatile tool for accessing and analyzing pathways using standard systems biology formats

Eric BonnetComputational Systems Biology of Cancer

Institut Curie - INSERM U900 - Mines ParisTech

http://sysbio.curie.fr

Workshop NUS-IBENS 30/05/2013

Pathway databases

Molecular reactions maps

RB / E2F map

Standard formats

BiNoM, a Biological Network Manager

• 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.

BiNoM Utilities

BiNoM Structure analysis

BiNoM BioPAX Query

BiNoM I/O

BiNoM BioPAXUtilities

BiNoM Modules

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).

BiNoM

Modular representation

RB / E2F network, 70+ proteins, 160+ reactions, 350 publications

Modular representation

Invasive cancersNon-invasive cancers

• Influence graph G.• Input nodes I1, I2.• Output (target) node O1.

I1 -> B -> C -> O1I1 -> E -> C -> O1I2 -> E -> C -> O1

• Combinations of Interventions:

{C}, {E, B}, {I1, I2}

• Application of OCSANA: candidate drug targets discovery.

OCSANA: Optimal Combinations of Interventions for Network Analysis

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.

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