OCSANA: Optimal Combinations of Interventions from Network Analysis
 
Targeted therapies interfering specifically one protein activity, are promising strategies in the treatment of diseases like cancer. However, accumulated empirical experience has shown that targeting multiple proteins in signaling networks involved in the disease, is often necessary. Thus one important problem in biomedical research is the design and prioritization of optimal combinations of interventions to repress a pathological behavior, while minimizing side-effects. 

OCSANA (Optimal Combinations of Interventions from Network Analysis) is a new software designed to identify and prioritize optimal and minimal, combinations of interventions to disrupt the paths between source nodes and target nodes. When specified by the user, OCSANA seeks to additionally minimize the side-effects that a combination of interventions can cause on specified off-target nodes. With the crucial ability to cope with very large networks, OCSANA includes exact and selective enumeration approaches for the combinatorial interventions’ problem.

More information can be found at:

Vera-Licona P, Bonnet E, Barillot E, Zynovyev A. (2013) OCSANA: Optimal Combinations of Interventions from Network Analysis. Bioinformatics, 29 (12): 1571-1573. http://bioinformatics.oxfordjournals.org.gate2.inist.fr/content/29/12/1571.longhttp://bioinformatics.oxfordjournals.org.gate2.inist.fr/content/29/12/1571.longshapeimage_3_link_0shapeimage_3_link_1

OCSANA is a Cytoscape plugin under LGPL license. The latest version of OCSANA can be downloaded from here: OCSANA.jar. Once the OCSANA.jar file is downloaded, it has to be put into the Plugins Folder contained in Cytoscape.


The source code  can be downloaded from here: Ocsana_src.tar.


NOTE: If you have installed the latest version of BiNoM, OCSANA is already included in its menu! Currently it is under  BiNoM’s Experimental Release.

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Tutorial

Performance Analysis

Introduction

Screenshot

This tutorial contains a description of the terms, parameters and features in OCSANA’s software. It can be downloaded here: Tutorial.pdf.


The tutorial includes a walkthrough example. All the files for this example, including the Cytoscape file of the network itself can be downloaded here: WalkthroughExample.zip.

To test OCSANA’s performance, we used three biological networks. The full performance analysis (including the Cytoscape files of the networks) can be downloaded from here: PerformanceAnalysis.zip.

Acknowledgements

This work is supported by the ASSET EU FP7 collaborative project under grant n° 259348 from call FP7-HEALTH-2010-two-stage, and by the grant “Projet Incitatif et Collaboratif Computational Systems Biology Approach for Cancer” from Institut Curie. PVL, ErB, EmB and AZ are members of the team “Computational Systems Biology of Cancer”, Equipe labellisée by La Ligue Nationale Contre le Cancer.



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OCSANA’s Team

Contact Information

Paola Vera-Licona (Computational Systems Biology of Cancer, Institut Curie. Paris)