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BiNoM Tutorial
Andrei Zinovyev, Laurence CalzoneUMR U900 INSERM/Institut Curie/Ecole des Mines de Paris
Wednesday, April 30th
Install and Start Cytoscape+BiNoM
1) Download Cytoscape installer version 2.4.0 from http://cytoscape.org
2) Download BiNoM from
http://bioinfo-out.curie.fr/projects/binom/BiNoM_all.jar
3) Copy BiNoM_all.jar into the ‘plugins’ folder of Cytoscape
4) Remove (better, backup) xercesImpl.jar from the ‘lib’ folder of Cytoscape
Attention : BiNoM is not yet compatible with the latest version of Cytoscape 2.6.0. These technical issues will be resolved very soon.
Choose in the menuPlugins / BiNoM Analysis / Monomolecular reactions to edges
Initial network Result of operation
Choose in the menu Plugins / BiNoM Analysis / Exclude intermediate nodes
Initial network Result of operation
1. Select NFkB@nucleus and IkB_alpha:NFkB nodes (holding Shift key)2. Choose in the menu: Plugins / BiNoM Analysis / Path analysis
1. Select NFkB@nucleus and IkB_alpha:NFkB nodes (holding Shift key)2. Choose in the menu: Plugins / BiNoM Analysis / Path analysis
Biological PAthway eXchange format
BioPAX
Molecular InteractionsPro:Pro All:All
PSI
Biochemical Reactions
SBML,CellML
Regulatory PathwaysLow Detail High Detail
GeneticInteractions
Interaction NetworksMolecular Non-molecularPro:Pro TF:Gene Genetic
Metabolic PathwaysLow Detail High Detail
DatabaseExchange Formats
Simulation ModelExchange Formats
SmallMolecules (CML)
RateFormulas
Get BioPAX annotationBiNoM BioPAX Utils/BioPAX Property Editor
Browse by clicking at the color labels
Exporting subnetwork: 3. Plugins->BiNoM->Export current network to BioPAX
4. Associate with MAPK_Reactome5. Save to ERK2.owl
Pathway Database -> BioPAX -> BiNoM query
Cancer Cell Map
Reactome
BioBase
INOH
HumanCyc
Nature/NCI Pathway Interaction
KEGG
BiNoM
Big BioPAX
file
To work with big BioPAX file, BiNoM user should generate BioPAX index
Reactome.owl file
ReactomeIndex
.xgmml fileBiNoM BiNoM
Query
Network
Loading index:Plugins / BiNoM BioPAX Query / Load Index
The accession number file(list of synonyms) is optional.It facilitates identifying proteinsby name or other Ids
Plugins / BiNoM Analysis / Extract Reaction Network
Plugins / BiNoM Analysis / Mono-molecular Reactions To Edges
Simplifying the query result view
Finding the shortest path from one protein to anotherPlugins / BiNoM BioPAX Query / Index Path Analysis
Finding the shortest path and suboptimal path from one protein to anotherPlugins / BiNoM BioPAX Query / Index Path Analysis
1) Select nodes2) Open dialog, change parameters
3) Apply hierarchic layout
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