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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