Cytoscape 3Architecture, Current Status, and Future Plan

Keiichiro OnoUniversity of California, San Diego

Trey Ideker Lab

Who am I?- Keiichiro Ono

- Cytoscape Core Developer since 2005- University of California, San Diego Trey

Ideker Lab

Outline

- Why Cytoscape 3?- Architecture- Current Status- Future Plan

Quick Introduction to Cytoscape

- Open source platform for biological network- data integration- analysis- visualization

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Plugins Apps

AllegroMCODE APCluster APID2NET BioQualiPlugin BLAST2SimilarityGraph BNMatch CABIN CalculateNodeDegree CentiScaPe ChemViz clusterExplorerPlugin clusterMaker ClusterONE ClusterViz COMA CommFinder CyClus3D CyOog cytoHubba Cytomcl DualLayout dynamicXpr EnhancedSearch EnrichmentMap ExprEssence GraMoFoNe GraphletCounter HiderSlider jActiveModules mcl-new MCODE MINE NeMo NetAtlas NetCirChro netMatch NetworkAnalyzer NetworkEvolut ion OmicsAnalyzer OmicsViz OrthoNets PanGIA Per turbat ionAna lyzer P innac leZ RandomNetworks RDFScsape Reactome F Is RemainingDegreeDistribution ReOrientPlugin ShortestPath Plugin SimTrek structureViz TransClust VennDiagramGenerator VistaClaraPlugin WordCloud BiNoM bioCycPlugin Biogr idPlugin BiomartCl ient BioNetBui lder BisoGenet ConsensusPathDBplugin CoryneRegNetLoader CyThesaurus-ID-Mapping CytoSQL DroID Genoscape GPML-Plugin GraphMLReader IntActWSClient iRefScape KGMLReader MetScape MiMIplugin NCBIClient NCBIEntrezGeneUserInterface Pathintegrator PhosphositePlus Web Service Client Module PICRClient PSICQUICUniversalClient ReConn SessionForWeb SFLDLoader StringWSClient Superpathways-Plugin 3DScape Agi lentLiteratureSearch Cytoprophet DisGeNET DomainGraph ExpressionCorrelation GeneMANIA MetaNetter MONET BiNGO BubbleRouter ClueGO CommonAttributes DisplayNetworkFromFlatFile FluxViz FunNetViz HyperEdgeEditor PiNGO CyGoose CytoscapeRPC GroovyScriptingEngine JavaScriptEngine MiSink PythonScriptingEngine RubyScriptingEngine ScriptEngineManager addParentNeighbors AdvancedNetworkMerge batchTool BiLayout commandTool coreCommands CyAnimator edgeLengthPlugin edgeLister EpiTrace FERN FM3 GoogleChartFunctions GroupTool MetaNodePlugin2 Multi levelLayoutPlugin NamedSelection NatureProtocolsWorkflow NeighborHighlight NetLink nodeCharts PhyloTree VennDiagrams

140+ Apps

- One of the most successful applications in systems biology field

- Large user/developer community

Why Cytoscape 3?

C

Problems

Problems

- Apps can’t use conflicting libraries

?!Apache httpcomponents-client-4.1.2 GA

App 1

Apache httpcomponents-client-4.0.3

App 2

Problems

- Apps can’t publish their API

public int calculateDegree()

App 1

public void setNodeSizeByDegree()

App 2

No clean way to access!

Why these are serious?- Reinventing the wheel

- Even if other apps have nice features, there is no standard way to access those (programmatically)

- Crash!- Cytoscape will be unstable if plugins have

conflicting libraries

Backward Compatibility

- Cytoscape core updates break plugins- No clear definition of API- Versioning

AllegroMCODE APCluster APID2NET BioQualiPlugin BLAST2SimilarityGraph BNMatch CABIN CalculateNodeDegree CentiScaPe ChemViz clusterExplorerPlugin clusterMaker ClusterONE ClusterViz COMA CommFinder CyClus3D CyOog cytoHubba Cytomcl DualLayout dynamicXpr EnhancedSearch EnrichmentMap ExprEssence GraMoFoNe GraphletCounter HiderSlider jActiveModules mcl-new MCODE MINE NeMo NetAtlas NetCirChro netMatch NetworkAnalyzer NetworkEvolution OmicsAnalyzer OmicsViz OrthoNets PanGIA PerturbationAnalyzer PinnacleZ RandomNetworks RDFScsape Reactome FIs RemainingDegreeDistribution ReOrientPlugin ShortestPath Plugin SimTrek structureViz TransClust VennDiagramGenerator VistaClaraPlugin WordCloud BiNoM bioCycPlugin BiogridPlugin BiomartClient BioNetBuilder BisoGenet ConsensusPathDBplugin CoryneRegNetLoader CyThesaurus-ID-Mapping CytoSQL DroID Genoscape GPML-Plugin GraphMLReader IntActWSClient iRefScape KGMLReader MetScape MiMIplugin NCBIClient NCBIEntrezGeneUserInterface Pathintegrator PhosphositePlus Web Service Client Module PICRClient PSICQUICUniversalClient ReConn SessionForWeb SFLDLoader StringWSClient Superpathways-Plugin 3DScape AgilentLiteratureSearch Cytoprophet DisGeNET DomainGraph ExpressionCorrelation GeneMANIA MetaNetter MONET BiNGO BubbleRouter ClueGO CommonAttributes DisplayNetworkFromFlatFile FluxViz FunNetViz HyperEdgeEditor PiNGO CyGoose CytoscapeRPC GroovyScriptingEngine JavaScriptEngine MiSink PythonScriptingEngine RubyScriptingEngine ScriptEngineManager addParentNeighbors AdvancedNetworkMerge batchTool BiLayout commandTool coreCommands CyAnimator edgeLengthPlugin edgeLister EpiTrace FERN FM3 GoogleChartFunctions GroupTool MetaNodePlugin2 Multi levelLayoutPlugin NamedSelection NatureProtocolsWorkflow NeighborHighlight NetLink nodeCharts PhyloTree VennDiagrams

Solutions

- OSGi- Enforce modularity

- Semantic Versioning- Manage the changes

- Maven- Organize build/release process

Architecture

Overview

Java Virtual Machine

OSGi Framework

Cytoscape API Bundle A

Cytoscape API Bundle B

Cytoscape API Bundle CLib 1 Lib 2

Cytoscape Impl Bundle A Cytoscape Impl Bundle CCytoscape Impl Bundle B

App 1 App 2 App YApp X

OSGi Framework

−Provides runtime container

−Defines module boundaries

−Provides micro service architecture

Collection of Modules

OSGi Module

= Bundle

= JAR + Metadata

Defines what packages are visible from othersExport-Packages: org.cytocape.model

Defines which modules are required to use thisImport-Packages: org.cytoscape.events

Module X Module YModule Z

API 1

API 2

API 3

Defines public API

OSGi Service

= Shared Java Object Instances

OSGi Service

xyz IMPLxyz API

abc IMPL

abc API

Your App

IMPL modules register instances of service interfaces with the Service Registry

Service Registry

Apps depend on classes and service interfaces defined in the API

Apps get on instances of services interfaces from the Service Registry usingONLY the service interfaces!

IMPL modules create instances of service interfaces defined in the API

Cytoscape +

OSGi

Semantic Versioning

- Version number has meaning!

- major.minor.patch- patch - backwards compatible bug fixes

- minor - backwards compatible new features

- major - backwards incompatible changes

Maven

- Build tool- Manages dependencies

- Cytoscape Maven Repository

Summary

- OSGi enforces you to use modular design- Semantic versioning defines how and

when changes happen- Maven provides easy access to correct

version of libraries in the build process

Designing your Apps for 3

Design Guidelines for App Developers

- Define API as a collection of interfaces- Do not publish implementation details- Export useful objects as OSGi services

Future Plan

What can we do with 3?

- Use Cytoscape modules as a building blocks of other applications

- Add/replace modules- New rendering engines- Graph database backend

Upcoming Projects- New Rendering Engine- Smart Zooming (like Google Map)- Headless/command-line Mode

- Run Cytoscape 3 on clouds- R/Matlab Integration- Graph Database Integration (Neo4j via

Tinkerpop Blueprints)- Publish to cytoscape.js

Release Schedule- Milestone 5 Released - For app developers- User Beta - Late September- User Beta 2- 3.0 Final Release

- At Cytoscape Retreat 2012 @UCSF- December 13, 14

Where to Start?

- http://wiki.cytoscape.org/Cytoscape_3- http://code.cytoscape.org

NIH GM070743-01

P01 HG005062

P41 RR031228

www.cytoscape.org