netbiosig2012 mikesmoot

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Cytoscape is a popular, open source desktop application for visualizing and analyzing biological networks. Cytoscape 2.X consists of a core application that provides a visualization and analysis capabilities along with an API for extending Cytoscape’s functionality through “plugins.” Scientists and other Cytoscape users benefit from the analytical depth provided by the plugins, while plugin authors benefit from the core Cytoscape functionality and the framework for distributing and advertising plugins. This mutually beneficial relationship has resulted in over 150 plugins (http://cytoscape.org/plugins.html) along with dozens of publications about the plugins themselves.Cytoscape 3.0 represents an attempt to refactor Cytoscape to make app writing (plugins will be renamed “apps” in 3.0) simpler while at the same time providing more stability, power, and flexibility to the system as a whole. First and foremost, Cytoscape 3.0 has been modularized with the API cleanly separated from the implementation. This modularity is being facilitated and enforced with OSGi (http://osgi.org), a popular Java modularization framework. OSGi’s micro service architecture allows private implementation code to remain private by registering micro services, which rely only on the public API. This means that any app only has the opportunity to depend on the public API, which will hopefully clarify and simplify what is needed to write an app. We have also begun using the Semantic Versioning standard (http://semver.org) for Cytoscape code to make clear how and when a public API may change. This will all go towards helping the Cytoscape core maintain backwards compatibility, which will greatly increase app stability. All “apps” in 3.0 can be written as OSGi bundles, just like the Cytoscape core modules. This means that apps will now have the opportunity to register their own public API, eliminating the distinction between core and app and resulting in a much more powerful and flexible system. While the architecture of Cytoscape 3.0 relies on OSGi, very little code does. While not without risk, we believe that Cytoscape 3.0 will enable a new generation of Cytoscape apps as well as much greater opportunity for collaboration with different systems. This talk will elaborate on the new Cytoscape architecture including its benefits, challenges, and risks.

TRANSCRIPT

Architecture for Extension

Michael Smoot Ph.D.Cytoscape Chief Architect

ISMB NetBIO SIG July 13, 2012

Thursday, July 19, 2012

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Desktop Application written in Java

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3Biological Network Visualization + AnalysisThursday, July 19, 2012

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Free Software - LGPL

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5~5000 downloads per monthThursday, July 19, 2012

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7Photo credit: Samuel L. Livingston

Cytoscape’s most important feature?

Our Plugin App Architecture

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Builds a community of stakeholders

Apps allow for customization

Primary analysis mechanism

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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 M O N E T B i N G O B u b b l e R o u t e r C l u e G O C o m m o n A t t r i b u t e s DisplayNetworkFromFlatFile FluxViz FunNetViz HyperEdgeEditor PiNGO CyGoose C y t o s c a p e R P C G r o o v y S c r i p t i n g E n g i n e J a v a S c r i p t E n g i n e M i S i n k P y t h o n S c r i p t i n g E n g i n e R u b y S c r i p t i n g E n g i n e S c r i p t E n g i n e M a n a g e r addParentNeighbors AdvancedNetworkMerge batchTool BiLayout commandTool coreCommands CyAnimator edgeLengthPlugin edgeLister EpiTrace FERN FM3 GoogleChartFunctions GroupTool MetaNodePlugin2 MultilevelLayoutPlugin NamedSelection NatureProtocolsWorkflow NeighborHighlight NetLink nodeCharts PhyloTree VennDiagrams

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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 M O N E T B i N G O B u b b l e R o u t e r C l u e G O C o m m o n A t t r i b u t e s DisplayNetworkFromFlatFile FluxViz FunNetViz HyperEdgeEditor PiNGO CyGoose C y t o s c a p e R P C G r o o v y S c r i p t i n g E n g i n e J a v a S c r i p t E n g i n e M i S i n k P y t h o n S c r i p t i n g E n g i n e R u b y S c r i p t i n g E n g i n e S c r i p t E n g i n e M a n a g e r addParentNeighbors AdvancedNetworkMerge batchTool BiLayout commandTool coreCommands CyAnimator edgeLengthPlugin edgeLister EpiTrace FERN FM3 GoogleChartFunctions GroupTool MetaNodePlugin2 MultilevelLayoutPlugin NamedSelection NatureProtocolsWorkflow NeighborHighlight NetLink nodeCharts PhyloTree VennDiagrams

Thursday, July 19, 2012

11

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 M O N E T B i N G O B u b b l e R o u t e r C l u e G O C o m m o n A t t r i b u t e s DisplayNetworkFromFlatFile FluxViz FunNetViz HyperEdgeEditor PiNGO CyGoose C y t o s c a p e R P C G r o o v y S c r i p t i n g E n g i n e J a v a S c r i p t E n g i n e M i S i n k P y t h o n S c r i p t i n g E n g i n e R u b y S c r i p t i n g E n g i n e S c r i p t E n g i n e M a n a g e r addParentNeighbors AdvancedNetworkMerge batchTool BiLayout commandTool coreCommands CyAnimator edgeLengthPlugin edgeLister EpiTrace FERN FM3 GoogleChartFunctions GroupTool MetaNodePlugin2 MultilevelLayoutPlugin NamedSelection NatureProtocolsWorkflow NeighborHighlight NetLink nodeCharts PhyloTree VennDiagrams

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So whatʼs the problem?

12Photo credit: TaekwonweirdoPhoto credit: Dean247

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Thursday, July 19, 2012

14Photo credit: TaekwonweirdoPhoto credit: Dean247

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16Photo credit: Taekwonweirdo

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!!! A tangled mess of inter-dependencies

!!! Every public class is part of the API

!!! Backwards compatibility is impossible

!!! Poor deprecation and versioning strategy

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Is that all?

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!!! Apps canʼt use conflicting libraries

!!! Apps canʼt publish their own APIs

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Hurts core developers,app writers, and users!

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How do we fix this?

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1. OSGi

2. Semantic Versioning

3. Maven

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Cytoscape 3.0

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Cytoscape 3.0 Milestone 5 is available here:

http://cytoscape.org

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http://cytoscape.org
http://cytoscape.org

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OSGi− provides

runtime container

− defines module boundaries

− provides micro service architecture

Cytoscape Application Stack

Java Virtual Machine

OSGi Framework

Cytoscape API Bundle A

Cytoscape API Bundle B

Cytoscape API Bundle C

Lib 1

Lib 2

Cytoscape Impl Bundle A

Cytoscape Impl Bundle C

Cytoscape Impl Bundle B

App 1 App 2 App YApp X

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How does OSGi accomplish this?

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Module = Jar + Metadata

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Defines what can depend on the module.Export-Packages: org.cytocape.model

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Defines what the module can depend on.Import-Packages: org.cytoscape.events

Module X Module YModule Z

API 1

API 2

API 3

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Independence

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Module AModule C

Module B

Library X v 1.1

Module K

Module Z

Module M

Library X v 1.2

Every App gets its own Classloader!

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μServices

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xyz IMPL

xyz 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

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OSGienables

Modularity

32Photo credit: Maurice Koop

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OSGi enforces Modularity

33Photo credit: BlackmanVision

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Semantic Versioning:

34

Version numbers have meaning!

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VERSION: major.minor.patch

patch - backwards compatible bug fixes

minor - backwards compatible new features

major - backwards INcompatible changes

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As long as we version honestly, your app will always work!

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(At least until the next major version update)

Because versions have a functional meaning, we can reason about ranges

[3.1,4)

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Maven

Organize

Build

Release

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1. OSGi

2. Semantic Versioning

3. Maven

- To enable/enforce modularity

- To define how and when changes happen

- To organize, build, and release

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1. Clearly define API

2. Enforce separation of API and implementation

3. Clearly define what can change and when

4. Sensible dependencies

5. Make writing and maintaining plugins easy

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For more information visit:

http://cytoscape.org

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http://cytoscape.org
http://cytoscape.org

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NIH GM070743-01

P01 HG005062

P41 RR031228

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Thank you!

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Any Questions?

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Climber

No ropes!!!Risks?

Photo credit: notorious d.a.v.

Lose momentum in lengthy rewrite?

Is the new API too limiting?

Porting apps more trouble than itʼs worth?

Is OSGi just too complicated?

Thursday, July 19, 2012

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