1 / 28

BI ological N etw O rk M anager Cytoscape plugin

BI ological N etw O rk M anager Cytoscape plugin. Andrei Zinovyev Institut Curie/INSERM/Ecole de Mines, UMR 900 “Computational Systems Biology of Cancer” http://bioinfo.curie.fr/sysbio. BiNoM purpose in two words. …very user friendly, but the possibilities to

remedy
Download Presentation

BI ological N etw O rk M anager Cytoscape plugin

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. BIological NetwOrk Manager Cytoscape plugin Andrei Zinovyev Institut Curie/INSERM/Ecole de Mines, UMR 900 “Computational Systems Biology of Cancer” http://bioinfo.curie.fr/sysbio ICSB Web-services - 28 August 2008

  2. ICSB Web-services - 28 August 2008

  3. BiNoM purpose in two words …very user friendly, but the possibilities to analyze and manipulate the diagram are limited CellDesigner • BiNoM: • Easy manipulations of SB standards • Cytoscape environment • Java library decoupled from GUI • Tools for network analysis …very interactive, but the support of existing Systems biology standards is very limited Cytoscape BioPAX …very useful, but no easy tools for creating and editing ICSB Web-services - 28 August 2008

  4. BiNoM platform (Zinovyev et al., Bioinformatics, 2008) BiNoM BioPAX Utilities BiNoM I/O BiNoM Structure analysis BiNoM BioPAX Query BiNoM Utilities Some Functions of the version 1.0: Import of BioPAX, SBML, CellDesigner and simple influence network formats Export to BioPAX, SBML and CellDesigner formats after user manipulations Network clipboard Conversion between standards (CellDesigner->BioPAX, BioPAX->SBML) Full support of BioPAX information (reaction network, interaction network, pathway structure, references) Editing BioPAX content Structural analysis of the networks (extracting strongly connected components, clustering relevant cycles, structural pathway analysis, modular network representation, path analysis) Biological network databases query system ICSB Web-services - 28 August 2008

  5. Typical scenarios • Import CellDesigner diagram, manipulate, convert to BioPAX • Import CellDesigner diagram, put colors and save it back • Import CellDesigner diagram, analyze, decompose into modules, create a modular view of the diagram • Import BioPAX file, extract a part, export to SBML, create a model • Import BioPAX file, edit, save it back • Index huge BioPAX file (whole Reactome), make a query, save result as small BioPAX file • Create a new BioPAX file from simple text file • etc. ICSB Web-services - 28 August 2008

  6. Standard SB file BiNoM interfaces (subgraphs) BiNoM index (attributed graph) BiNoM query mechanism (extract subgraph) BiNoM notion of network index ICSB Web-services - 28 August 2008

  7. Limited SBGN notation support

  8. Naming convension

  9. 1: Working with CellDesigner files (importing/converting) BioPAX ICSB Web-services - 28 August 2008

  10. 1: Working with CellDesigner files (analysis) Graph pruning, extracting strongly connected components, decomposition into cycles, finding shortest, subpotimal, all paths, clustering subgraphs, etc... Calzone et al. Comprehensive modular map of RB/E2F pathway. Molecular Systems Biology, 2008

  11. 1: Working with CellDesigner files (coloring)

  12. 1: Working with CellDesigner files (generating web-sites) http://bioinfo.curie.fr/projects/rbpathway

  13. 2: Working with BioPAX files ICSB Web-services - 28 August 2008

  14. Reaction network representation reactions proteins (species) complexes (species) ICSB Web-services - 28 August 2008

  15. Pathway structure representation pathway Pathway step ICSB Web-services - 28 August 2008

  16. ‘Protein interactions’ representation proteins (entities) complexes (entities) ICSB Web-services - 28 August 2008

  17. Basic BioPAX editor

  18. Pathway Database -> BioPAX -> BiNoM query Reactome Cancer Cell Map Big BioPAX file INOH BiNoM Nature/NCI Pathway Interaction BioCyc Pathway Commons BioBase

  19. To work with big BioPAX file, BiNoM generates index (connection graph) Reactome Index .xgmml file Query Reactome .owl file BiNoM BiNoM Network

  20. Example of query

  21. Examples of query … Give all interactions in which IGF1 participates … Give all interactions connecting given proteins

  22. … Give the shortest path connecting given proteins

  23. … Give the shortest and suboptimal paths connecting given proteins Export to BioPAX Export to SBML

  24. Create BioPAX file from a simple text file (Facts sheet) 2) Consistency check 1) Defining families

  25. Create BioPAX file from a simple text file (Facts sheet) Export to BioPAX Export to SBML

  26. Nearest future development • BioPAX 3.0 support • CellDesigner format 4.0 support • Creating BiNoM plug-in for CellDesigner 4.0 • New structural analysis algorithms ICSB Web-services - 28 August 2008

  27. Install and Start Cytoscape+BiNoM Note: BiNoM is not yet compatible with the latest version of Cytoscape 2.6.0. These technical issues will be resolved very soon Detailed manual + Tutorial are available! Reference: Zinovyev et al, Bioinformatics 2008

  28. Acknowledgements Eric Viara Laurence Calzone Gautier Stoll Emmanuel Barillot EU FP6 project ESBIC-D (LSHG-CT-2005-518192) High Council for Scientific and Technological Cooperation between France and Israel ICSB Web-services - 28 August 2008

More Related