binom tutorial
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BiNoM Tutorial
Andrei Zinovyev, Laurence CalzoneUMR U900 INSERM/Institut Curie/Ecole des Mines de Paris
Wednesday, April 30th
BiNoM is a plugin for Cytoscape
http://cytoscape.org/
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.
Starting course about Cytoscape
Short introduction into Cytoscape
Short introduction into Cytoscape
Selected nodes
Short introduction into Cytoscape
BiNoM – Biological Network Manager
Naming convension
Section 1. Basic Network Analysis tools in BiNoM
Importing CellDesigner (SBML) files
Open NFKB_final.xml example
Importing CellDesigner (SBML) files
Reaction network
Choose in the menuPlugins / BiNoM Analysis / Prune graph
Initial network Result of operation
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
Choose in the menu Plugins / BiNoM Analysis / Material components
NFkB
IkBInitial network
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
Section 2. BiNoM and BioPAX
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
BioPAXis formulated on Web Ontology
Language (OWL)
BioPAX level 2.0
Importing BioPAX files
Open example fileat Desktop/Pathway Charting/MAPK_Reactome.owl
Reaction network (RN)
Apply Layout -> yFiles -> Organic layout
Pathway hierachy (PS)
Apply Layout -> yFiles -> Hierarchic layout
Protein-protein interactions (PP)
Apply Layout -> yFiles -> Organic layout
Example of combined view
Apply Plugins->Merge networks
Alternative Pathway viewReimport the MAPK_Reactome example
with new pathway hierarchy options
Get BioPAX annotationPlugins / BiNoM BioPAX Utils/BioPAX Property Editor
Select someNodes first
Get BioPAX annotationBiNoM BioPAX Utils/BioPAX Property Editor
Browse by clicking at the color labels
Get Complete BioPAX annotationPlugins / BiNoM BioPAX Utils / BioPAX Class tree…
Exporting subnetwork: 1.Select subtree
2.File->New->Network->From selected nodes, all edges
Exporting subnetwork: 3. Plugins->BiNoM->Export current network to BioPAX
4. Associate with MAPK_Reactome5. Save to ERK2.owl
Exporting subnetwork: 6. Reopen ERK2.owl using Plugin->BiNoM I/O-> Import BioPAX
Section 3. Using BiNoM with pathway databases
Pathway Database -> BioPAX -> BiNoM query
Cancer Cell Map
Reactome
BioBase
INOH
HumanCyc
Nature/NCI Pathway Interaction
KEGG
BiNoMBig
BioPAXfile
To work with big BioPAX file, BiNoM user should generate BioPAX index
Reactome.owl file
ReactomeIndex
.xgmml fileBiNoM BiNoMQuery
Network
Preparing database: Plugins / BiNoM BioPAX Query / Generate Index
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 BioPAX Query -> Select entities IGF_1 IGFBP_3 pRB
Plugins / BiNoM BioPAX Query / Standard query
Get all reactions in which IGF_1 is involvedPlugins / BiNoM BioPAX Query / Standard query
Extract all selected reaction annotationsPlugins / BiNoM BioPAX Query / Standard query
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
Q: Why are there some hanging nodes in the tree?A: Because there are connections “through complexes”
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