BIological NetwOrk Manager Cytoscape plugin Andrei Zinovyev Institut Curie/INSERM/Ecole de Mines,...

BIological NetwOrk Manager Cytoscape plugin

Andrei ZinovyevInstitut Curie/INSERM/Ecole de Mines, UMR 900

“Computational Systems Biology of Cancer”http://bioinfo.curie.fr/sysbio

ICSB Web-services - 28 August 2008

ICSB Web-services - 28 August 2008

BiNoM purpose in two words

ICSB Web-services - 28 August 2008

BioPAX

CellDesigner

Cytoscape

…very user friendly, but the possibilities to analyze and manipulate the diagram are limited

…very interactive, but the support of existingSystems biology standards is very limited

…very useful, but no easy tools for creating and editing

BiNoM:1)Easy manipulations of SB standards2)Cytoscape environment3)Java library decoupled from GUI4)Tools for network analysis

ICSB Web-services - 28 August 2008

BiNoM platform (Zinovyev et al., Bioinformatics, 2008)

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

BiNoM I/O

BiNoM Utilities

BiNoM Structure analysis

BiNoM BioPAX Query

BiNoM BioPAX Utilities

Typical scenarios

ICSB Web-services - 28 August 2008

1) Import CellDesigner diagram, manipulate, convert to BioPAX

2) Import CellDesigner diagram, put colors and save it back

3) Import CellDesigner diagram, analyze, decompose into modules, create a modular view of the diagram

4) Import BioPAX file, extract a part, export to SBML, create a model

5) Import BioPAX file, edit, save it back

6) Index huge BioPAX file (whole Reactome), make a query, save result as small BioPAX file

7) Create a new BioPAX file from simple text file

etc.

BiNoM notion of network index

ICSB Web-services - 28 August 2008

BiNoM index (attributed graph)

BiNoM interfaces (subgraphs)

BiNoM query mechanism (extract subgraph)

Standard SB file

Limited SBGN notation support

Naming convension

1: Working with CellDesigner files (importing/converting)

ICSB Web-services - 28 August 2008

BioPAXBioPAX

1: Working with CellDesigner files (analysis)

Calzone et al. Comprehensive modular map of RB/E2F pathway. Molecular Systems Biology, 2008

Graph pruning, extracting strongly connected components, decomposition into cycles, finding shortest, subpotimal, all paths, clustering subgraphs, etc...

1: Working with CellDesigner files (coloring)

1: Working with CellDesigner files (generating web-sites)

http://bioinfo.curie.fr/projects/rbpathway

2: Working with BioPAX files

ICSB Web-services - 28 August 2008

ICSB Web-services - 28 August 2008

Reaction network representation

reactions

proteins (species)

complexes (species)

ICSB Web-services - 28 August 2008

Pathway structure representation

pathway

Pathway step

ICSB Web-services - 28 August 2008

‘Protein interactions’ representationproteins (entities)

complexes (entities)

Basic BioPAX editor

Pathway Database -> BioPAX -> BiNoM query

Cancer Cell Map

Reactome

BioBase

INOH

BioCyc

Nature/NCI Pathway Interaction

Pathway Commons

BiNoM

Big BioPAX

file

To work with big BioPAX file, BiNoM generates index (connection graph)

Reactome.owl file

ReactomeIndex

.xgmml fileBiNoM BiNoM

Query

Network

Example of query

Examples of query

… Give all interactions in which IGF1 participates

… Give all interactions connecting given proteins

… Give the shortest path connecting given proteins

Export to BioPAXExport to SBML

… Give the shortest and suboptimal paths connecting given proteins

Create BioPAX file from a simple text file (Facts sheet)

1) Defining families 2) Consistency check

Create BioPAX file from a simple text file (Facts sheet)

Export to BioPAXExport to SBML

Nearest future development

ICSB Web-services - 28 August 2008

1) BioPAX 3.0 support

2) CellDesigner format 4.0 support

3) Creating BiNoM plug-in for CellDesigner 4.0

4) New structural analysis algorithms

Install and Start Cytoscape+BiNoM

Note: BiNoM is not yet compatible with the latest version ofCytoscape 2.6.0. These technical issues will be resolved very soon

Detailed manual + Tutorial are available!

Reference: Zinovyev et al, Bioinformatics 2008

Acknowledgements

ICSB Web-services - 28 August 2008

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