Introduction to Cytoscape @Sanford Consortium Auditorium 12/6/2013

Introduction to Cytoscape and quick review of Cytoscape 3.1.0.

Transcript

1. Cytoscape
   ! An Open Source Platform
   for Biological Network Analysis and Visualization
   ! SDCSB Workshop 12/6/2013 Keiichiro Ono Cytoscape Core Developer Team University of California, San Diego Trey Ideker Lab
2. Welcome! - Keiichiro Ono - Cytoscape Core Developer since 2005 - Core module design & implementation - Area of Interest: Data Integration & Visualization
3. Schedule - My presentation - Basic Introduction to Cytoscape and new Features in ver. 3.1.0 - Tutorial Sessions - For Beginners - For Experienced Users
4. Workshop - For Beginners (By Rintaro & Barry) - Basic features of Cytoscape - Load data, create Visual Style, layout, etc. - Hands-on style - For Experienced Users (By Me) - How to create good visualization with Cytoscape - Lecture style - More introduction to new features in Cytoscape 3.1 and Cytoscape.js
5. Made on…
6. Agenda - What is Cytoscape? - How Cytoscape helps your research projects - Cytoscape 3.1 Intro.
7. What is Cytoscape?
8. Cytoscape - Open source platform for biological network data integration, analysis, and visualization
10. - Free! (open source, LGPL) - Developed and maintained by universities, companies, and research institutions - De-facto standard software in biological network research - Expandable by Apps
11. Networks in Biology?
12. Network = Nodes + Edges G=(V, E)
13. Protein-Protein Interaction
14. Human-Curated Pathways KEGG Pathway Visualized by Cytoscape
15. Interactome
16. M20 M10 M18 M9 M19 M12 M7 M6 M17 M2 M15 M5 M11 M4 M8 M1 M3 M16 M13 M14 Network of 
 Biological Modules
17. Collection of Relations = Network
18. Nodes and Edges in Biology - Protein - Protein - Protein - DNA - Genetic (Epistasis) - Synthetic lethality - Biochemical Reactions - Compound - Enzyme - Compound Cartoon representation of a complex between DNA and the protein p53 Node Node Edge
19. Undirected Network - Protein - Protein Interaction
20. Directed Network KEGG Pathway (TCA Cycle) visualized by Cytoscape KGMLReader
21. KEGG Global Map Visualized by Cytoscape
22. Cytoscape is Domain- Independent
23. Twitter Visualization
24. The Challenge in Network Biology
26. BioGRID Mouse Network Release 3.2.95 - 5.5k nodes / 13k edges ?
27. Biological Networks - Tell us anything by themselves - Big hairball (or small galaxy...)
29. In Other Words...
30. Networks
31. Genes of Interest
32. List of Drug Targets Other knowledge
34. Cytoscape is NOT a... - Simulator - Fully-featured Pathway diagram editor - There are good tools for it, like CellDesigner - Statistical network analysis tool suite - Still, you can use results from other applications, such as R
35. Our Focus
36. Large-Scale Network Analysis and Visualization Human Interactome data from BioGRID visualized by Cytoscape
37. Pick a Right Tool NetworkX
39. Summary - Cytoscape is a platform for: - Data integration: networks & known annotations, experimental/clinical data - Analysis: filter/search/module extraction - Visualization: Helps you to understand your data
40. Introduction to Biological Network Analysis Using Cytoscape
41. 1.Load Networks (Get network data) 2.Load Attributes (Get data about networks) 3.Analyze and Visualize Networks 4.Prepare for Publication - An example workflow: − Cline, et al. “Integration of biological networks and gene expression data using Cytoscape”, Nature Protocols, 2, 2366-2382 (2007). Cytoscape Workflow
42. Network Data Annotated Networks Attributes Analyzed Data Apps
43. <?xml version="1.0" encoding="UTF-8"?> <graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"> <!-- Created by igraph --> <key id="degree" for="node" attr.name="degree" attr.type="double"/> <key id="betweenness" for="node" attr.name="betweenness" attr.type="double"/> <graph id="G" edgedefault="directed"> <node id="n0"> <data key="degree">79</data> <data key="betweenness">0</data> </node> <node id="n1"> <data key="degree">9</data> <data key="betweenness">167</data> </node> <node id="n2"> <data key="degree">18</data> <data key="betweenness">75</data> </node> <node id="n3"> <data key="degree">8</data> <data key="betweenness">12</data> </node> <node id="n4"> <data key="degree">26</data> <data key="betweenness">210</data> </node> <node id="n5"> <data key="degree">29</data> <data key="betweenness">320</data> </node> Import Networks
44. Supported Network Data Formats - SIF - GML - XGMML - GraphML - BioPAX - PSI-MI - SBML - KGML (KEGG) - Excel - Delimited Text Table - CSV - Tab
45. I Don’t Have a Network! - In many cases, biologists start with a list of genes they are interested in, and they do not have interaction data for those - That’s OK — There are lots of public interaction databases - PPI, Genetic, co-expression, etc.
46. Understand Interaction Database - Each database has its speciality - Protein - Protein - STRING, IntAct - Genetic - BioGRID - Protein - Compound - ChEMBL - Human-Curated Pathways - KEGG, Reactome, PathwayCommons
47. Import Attributes
48. What are Attributes? - Any data that provides details about nodes, edges, and networks. - Annotation for the network
49. BRCA1 NCBI Gene ID 672 On Chromosome 17 GO Terms: DNA Repair Cell Cycle DNA Binding Ensemble ID ENSG00000012048
50. Node Attributes - Gene Expression Data - Human-readable gene names - Gene Ontology Terms
51. Edge Attributes - Interaction Detection Methods - Y2H, NMR, affinity chromatography, etc. - Interaction Type - Physical, genetic, predicted - Publication ID
52. Network Attributes - Experiment details - Pathway Metadata - Description - Publication ID
53. Public Data Source - Access directly from Cytoscape, or - Import as Table (Text/Excel)
54. Your Data Sets - Anything saved as a table can be loaded into Cytoscape - Excel - Tab Delimited Document - CSV - As long as proper mapping key is available, Cytoscape can map them to your networks.
55. Mapping Key in the Network Mapping Key in the Table
56. Analysis
57. Network Analysis - Filtering - Calculate network statistics by Network Analyzer - Degree distribution,centrality, etc. - Advanced analysis by Apps
58. Filtering - Find nodes and edges with specific conditions - Pick nodes with degree > 5 - Select edges extracted from publication X - Find nodes on KEGG Pathway X
62. New in 3.1: Fast Filtering - MUCH faster than last version - Simple User Interface
63. Visualization
64. ?
65. Biological Data Visualization - Help others to understand your data - Emphasize what you want to tell by the image - Use color, shape, size of objects effectively! - Excellent resource for data visualization - Tamara Munzner’s Web Site: 
 http://www.cs.ubc.ca/~tmm/
66. Core Idea - Map values to visual properties - Expression Value to Node Color - Edge Weight to Width - Degree to Node Size - Node Type to Shape
67. Map Attributes
    to Visual Properties
68. Visual Style - Collection of mappings from Attributes to Visual Properties New in 3.1: Re-designed Style Editor
69. Discrete Mapping Editor Continuous Mapping Editor
72. Layouts
73. New in 3.1: Updated PSICQUIC Client
74. Prepare for Publication - Network images can be exported as PDF/ PS/PNG/JPG. - Use PDF for your publications
75. Real World Examples http://cytoscape-publications.tumblr.com
76. Expanding Cytoscape with Apps
77. Cytoscape Apps - Extension programs to add new features to Cytoscape - Large app developer/user community - This is why Cytoscape is so successful in life science community
78. http://apps.cytoscape.org
80. 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 MultilevelLayoutPlugin NamedSelection NatureProtocolsWorkflow NeighborHighlight NetLink nodeCharts PhyloTree VennDiagrams 140+ Apps
81. App Example: BiNGO - The most popular Cytoscape App - Perform GO enrichment analysis and display the result (which terms are overrepresented in the selected region of network) visually
83. nucleocytoplasmic transport nuclear export RNA export from nucleus nucleic acid transport protein transport protein localization in nucleus cytoskeleton-dependent intracellular transport nucleobase, nucleoside, nucleotide and nucleic acid transport endosome transport intracellular protein transport nuclear transport intracellular transport protein localization in organelle cellular protein localization ribosome biogenesis ribosomal large subunit biogenesis organelle assembly ribonucleoprotein complex assembly macromolecular complex assembly cellular macromolecular complex subunit organization organelle organization membrane fusion cellular membrane fusion cytoskeleton organization SNARE complex disassembly vesicle fusion organelle fusion vesicle organization organelle inheritance vacuole organization cellular macromolecular complex disassembly cellular macromolecular complex assembly ribosome assembly ribosomal large subunit assembly ribosomal subunit assembly protein complex disassembly macromolecular complex disassembly protein complex assembly cellular protein complex assembly detoxification of cadmium ion detoxification of copper ion response to metal ion response to copper ion response to cadmium ion vacuole inheritance retrograde transport, endosome to Golgi protein targeting to peroxisome protein import vacuolar transport peroxisomal transport cellular protein complex disassembly early endosome to Golgi transport Golgi vesicle transport peroxisome organization CVT pathway protein targeting to vacuole protein import into peroxisome matrix, docking protein import into peroxisome matrix protein targeting response to reactive oxygen species cellular response to reactive oxygen species response to inorganic substance response to toxin spindle assembly checkpoint mitotic cell cycle spindle assembly checkpoint regulation of mitotic metaphase/anaphase transition negative regulation of mitotic metaphase/anaphase transition negative regulation of mitosis regulation of mitosis regulation of nuclear division negative regulation of cell cycle negative regulation of organelle organization negative regulation of cell cycle process mitotic cell cycle spindle checkpoint spindle checkpoint negative regulation of nuclear division mitotic cell cycle checkpoint regulation of mitotic cell cycle regulation of cell communication positive regulation of cell cycle process regulation of S phase negative regulation of cell communication regulation of microtubule cytoskeleton organization regulation of microtubule-based process positive regulation of spindle pole body separation regulation of transcription, DNA-dependent positive regulation of transcription by carbon catabolites regulation of cell projection assembly regulation of cell morphogenesis regulation of organelle organization negative regulation of cellular process regulation of cell cycle regulation of cytoskeleton organization regulation of cell cycle process regulation of spindle pole body separation negative regulation of cellular component organization regulation of signal transduction regulation of cellular process regulation of transposition regulation of transposition, RNA-mediated negative regulation of biological process regulation of cellular component organization positive regulation of transcription by galactose energy reserve metabolic process energy derivation by oxidation of organic compounds alditol metabolic process cellular glucan metabolic process carbohydrate phosphorylation glycolytic fermentation fermentation glycerol biosynthetic process glycogen metabolic process glucose catabolic process to ethanol glucose catabolic process ethanol metabolic process glucose metabolic process glycerol metabolic process hexose biosynthetic process galactose catabolic process galactose catabolic process via UDP-galactose galactose metabolic process gluconeogenesis monosaccharide biosynthetic process polyol biosynthetic process monohydric alcohol metabolic process polyol metabolic process glycolysis alditol biosynthetic process hexose metabolic process monosaccharide metabolic process hexose catabolic process monosaccharide catabolic process regulation of anatomical structure size regulation of cellular component size regulation of cell size DNA recombination reciprocal meiotic recombination mitochondrion degradation autophagy peptide or protein carboxyl-terminal blocking C-terminal protein lipidation mRNA metabolic process protein modification process RNA processing protein amino acid lipidation nuclear mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile post-translational protein modification phosphorus metabolic process carbohydrate metabolic process biosynthetic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process primary metabolic process cellular metabolic process catabolic process oxygen and reactive oxygen species metabolic process cellular catabolic process glucan metabolic process phosphate metabolic process cellular polysaccharide metabolic process cellular macromolecule biosynthetic process polysaccharide metabolic process RNA biosynthetic process phosphorylation gene expression macromolecule modification RNA metabolic process cellular protein metabolic process transcription metabolic process DNA metabolic process nucleic acid metabolic process cellular macromolecule metabolic process protein metabolic process macromolecule biosynthetic process macromolecule metabolic process protein amino acid phosphorylation general transcription from RNA polymerase II promoter lipoprotein biosynthetic process transcription from RNA polymerase II promoter transcription, DNA-dependent translation lipoprotein metabolic process cellular component disassembly protein complex biogenesis interphase cytokinesis cell communication cellular component biogenesis M phase meiosis response to abiotic stimulus cellular response to extracellular stimulus cellular response to stress response to external stimulus cellular response to external stimulus response to starvation response to stress cellular response to stimulus response to stimulus reproductive process growth sexual reproduction reproduction signaling process regulation of biological quality conjugation macroautophagy signaling biological_process response to chemical stimulus response to organic substance cellular response to oxidative stress cellular response to chemical stimulus response to extracellular stimulus response to pheromone response to oxidative stress response to nutrient response to nutrient levels cell cycle checkpoint response to temperature stimulus cellular response to starvation cellular response to nutrient levels signal transmission conjugation with cellular fusion reproductive cellular process response to pheromone involved in conjugation with cellular fusion signal transduction cellular response to nutrient cellular response to phosphate starvation regulation of initiation of mating projection growth regulation of phosphate metabolic process regulation of nucleotide catabolic process regulation of carbohydrate catabolic process regulation of nucleotide metabolic process regulation of metabolic process regulation of catabolic process positive regulation of nitrogen compound metabolic process regulation of nitrogen compound metabolic process regulation of cellular carbohydrate catabolic process regulation of polysaccharide metabolic process regulation of carbohydrate biosynthetic process regulation of glycolysis regulation of cellular carbohydrate metabolic process positive regulation of glycolysis regulation of carbohydrate metabolic process regulation of protein metabolic process regulation of glucan biosynthetic process regulation of polysaccharide biosynthetic process positive regulation of glucose metabolic process regulation of glycogen biosynthetic process regulation of glycogen metabolic process regulation of glucose metabolic process regulation of generation of precursor metabolites and energy regulation of DNA metabolic process regulation of macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of cellular protein metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of gene expression positive regulation of cellular carbohydrate metabolic process regulation of DNA-dependent DNA replication positive regulation of gene expression posttranscriptional regulation of gene expression regulation of translation positive regulation of cellular biosynthetic process positive regulation of macromolecule biosynthetic process regulation of DNA replication involved in S phase regulation of DNA replication regulation of cellular metabolic process regulation of transcription regulation of RNA metabolic process regulation of transcription from RNA polymerase II promoter positive regulation of transcription from RNA polymerase II promoter positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process positive regulation of metabolic process positive regulation of biological process positive regulation of transcription, DNA-dependent positive regulation of RNA metabolic process positive regulation of cellular process positive regulation of transcription positive regulation of cellular metabolic process positive regulation of cellular catabolic process positive regulation of carbohydrate metabolic process regulation of cellular catabolic process regulation of macromolecule metabolic process regulation of biosynthetic process positive regulation of catabolic process regulation of primary metabolic process regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process regulation of phosphorus metabolic process regulation of phosphorylation regulation of kinase activity regulation of GTP catabolic process regulation of transferase activity negative regulation of DNA binding regulation of purine nucleotide catabolic process regulation of molecular function heterotrimeric G-protein complex cycle regulation of binding negative regulation of binding negative regulation of transcription regulator activity regulation of transcription regulator activity regulation of DNA binding regulation of GTPase activity regulation of hydrolase activity negative regulation of transcription factor activity intracellular signal transduction small GTPase mediated signal transduction Ras protein signal transduction regulation of growth Rho protein signal transduction regulation of multi-organism process regulation of biological process regulation of localization regulation of signaling process regulation of anatomical structure morphogenesis regulation of transcription by galactose regulation of developmental process regulation of cellular component biogenesis regulation of cell projection organization regulation of mating projection assembly regulation of conjugation signal transduction involved in filamentous growth filamentous growth filamentous growth of a population of unicellular organisms regulation of conjugation with cellular fusion by signal transduction regulation of conjugation with cellular fusion RNA splicing, via transesterification reactions RNA splicing regulation of catalytic activity negative regulation of molecular function mRNA processing growth of unicellular organism as a thread of attached cells intracellular signaling pathway invasive growth in response to glucose limitation pheromone-dependent signal transduction involved in conjugation with cellular fusion cell surface receptor linked signaling pathway G-protein coupled receptor protein signaling pathway biological regulation signaling pathway regulation of transcription factor activity regulation of response to stimulus regulation of transcription by carbon catabolites regulation of transport multi-organism process meiosis I cell division cell cycle phase meiotic joint molecule formation cell cycle process localization cellular process membrane organization interphase of mitotic cell cycle cellular component organization cellular component assembly ribonucleoprotein complex biogenesis meiotic cell cycle M phase of meiotic cell cycle cell cycle macromolecular complex subunit organization homeostatic process establishment of mitotic spindle orientation establishment of protein localization glucose transport cellular localization hexose transport mitotic cell cycle establishment of localization establishment of mitotic spindle localization cellular membrane organization microtubule-based process establishment or maintenance of cell polarity cellular macromolecule localization establishment of RNA localization RNA localization establishment of spindle orientation establishment of localization in cell establishment of spindle localization establishment of organelle localization macromolecule localization cellular homeostasis actin filament-based process chemical homeostasis organelle localization cellular chemical homeostasis actin filament-based movement vesicle localization mRNA transport RNA transport protein localization spindle localization vesicle transport along actin filament iron assimilation by reduction and transport iron assimilation cellular iron ion homeostasis ion homeostasis di-, tri-valent inorganic cation homeostasis cellular di-, tri-valent inorganic cation homeostasis cation homeostasis cellular cation homeostasis cellular ion homeostasis iron ion homeostasis vesicle-mediated transport transport carbohydrate transport microtubule cytoskeleton organization establishment of cell polarity monosaccharide transport dicarboxylic acid metabolic process histidine family amino acid metabolic process serine family amino acid metabolic process histidine metabolic process carboxylic acid biosynthetic process amine biosynthetic process cellular amino acid metabolic process serine family amino acid biosynthetic process histidine family amino acid biosynthetic process cellular amino acid biosynthetic process tryptophan metabolic process aromatic amino acid family biosynthetic process indolalkylamine metabolic process chorismate metabolic process histidine biosynthetic process lipid oxidation fatty acid catabolic process lipid modification cellular lipid catabolic process fatty acid beta-oxidation fatty acid oxidation carboxylic acid catabolic process lipid catabolic process oxoacid metabolic process glutamine metabolic process fatty acid metabolic process arginine metabolic process glutamine family amino acid metabolic process carboxylic acid metabolic process nitrogen compound metabolic process amine metabolic process lipid metabolic process cellular amino acid derivative biosynthetic process alcohol catabolic process cellular aldehyde metabolic process cellular aromatic compound metabolic process carbohydrate biosynthetic process carbohydrate catabolic process cellular biogenic amine biosynthetic process small molecule biosynthetic process small molecule metabolic process cellular amine metabolic process indole derivative biosynthetic process aromatic compound biosynthetic process cellular biosynthetic process small molecule catabolic process cellular amino acid derivative metabolic process cellular nitrogen compound biosynthetic process organic acid biosynthetic process glyoxylate metabolic process heterocycle biosynthetic process indole derivative metabolic process monocarboxylic acid metabolic process cellular biogenic amine metabolic process aromatic amino acid family metabolic process tryptophan biosynthetic process pyruvate metabolic process generation of precursor metabolites and energy cellular carbohydrate catabolic process glyoxylate cycle cellular carbohydrate metabolic process alcohol biosynthetic process cellular carbohydrate biosynthetic process alcohol metabolic process indolalkylamine biosynthetic process organic acid catabolic process cellular ketone metabolic process cellular nitrogen compound metabolic process organic acid metabolic process cellular amino acid and derivative metabolic process cellular lipid metabolic process indole and derivative metabolic process heterocycle metabolic process
84. cytoskeleton-depen intracellular transp cellular protein localization cellular macromolecular complex subunit organization organelle organization cytoskeleton organization cellular response to reactive oxygen species regulation of anatomical structure size regulation of cellular component size regulation of cell size DNA recombination reciprocal meiotic recombination mitochondrion degradation autophagy cellular metabolic process catabolic process oxygen and reactive oxygen species metabolic process cellular catabolic process metabolic process cellular component disassembly protein complex biogenesis interphase cytokinesis cell communication cellular component biogenesis M phase meiosis response to abiotic stimulus cellular response to extracellular stimulus cellular response to stress response to external stimulus cellular response to external stimulus response to starvation response to stress cellular response to stimulus response to stimulus reproductive process growth sexual reproduction reproduction signaling process regulation of biological quality conjugation macroautophagy signaling biological_process response to chemical stimulus onse to organic substance cellular response to oxidative stress cellular response to chemical stimulus response to extracellular stimulus response to pheromone response to oxidative stress response to nutrient response to nutrient levels response to temperature stimulus cellular response to starvation cellular response to nutrient levels signal transmission conjugation with cellular fusion reproductive cellular process response to pheromone involved in conjugation with cellular fusion response to nutrient cellular response to phosphate starvation regulation of molecular function ction signal transduction involved in filamentous growth filamentous growth filamentous growth of a population of unicellular organisms regulation of conjugation with cellular fusion by signal transduction ith growth of unicellular organism as a thread of attached cells intracellular signaling pathway invasive growth in response to glucose limitation pheromone-dependent signal transduction involved in conjugation with cellular fusion cell surface receptor linked signaling pathway G-protein coupled receptor protein signaling pathway biological regulation signaling pathway multi-organism process meiosis I cell division cell cycle phase meiotic joint molecule formation cell cycle process localization cellular process membrane organization interphase of mitotic cell cycle cellular component organization cellular component assembly ribonucleoprotein complex biogenesis meiotic cell cycle M phase of meiotic cell cycle cell cycle macromolecular complex subunit organization homeostatic process establishment of mitotic spindle orientation establishment of protein localization glucose transport cellular localization hexose transport mitotic cell cycle establishment of localization establishment of mitotic spindle localization cellular membrane organization microtubule-based process establishment or maintenance of cell polarity cellular macromolecule localization establishment of RNA localization RNA localization establishment of spindle orientation establishment of localization in cell establishment of spindle localization establishment of organelle localization macromolecule localization cellular homeostasis actin filament-based process chemical homeostasis organelle localization ce actin filament-based movemen v mRNA transport RNA tra protein localization spindle localization transport carbohydrate transport microtubule cytoskeleton organization establishment of cell polarity monosaccharide transport cellular lipid catabolic p lipid catabolic process nitrogen compound metabolic process lipid metabolic process organic acid catabolic process cellular ketone metabolic process cellular
85. A Must Read A travel guide to Cytoscape plugins ! Rintaro Saito, Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng- Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader, Trey Ideker (2012) Nature Methods 9 (11) p. 1069-1076
86. Rintaro Saito et al: a travel guide to cytoscape plugins Nature Methods 9 (11) p. 1069-1076
87. Cytoscape Family
88. Cytoscape Family - Version 2.x - Legacy version - Version 3.x - Current - 3.0.x - Maintenance - 3.1.0 - Next release with new features - cytoscape.js - Library for web applications
89. New Features - New Style Editor - New High-Performance Filter - Commands - via REST - Export to Cytoscape.js - Updated Web Service Client (PSICQUIC)
90. Citation
91. 3.1 Overview
92. Cytoscape.js Network Visualization Library Running on Web Browsers
93. Cytoscape.js is NOT - Complete web application - Compatible with Cytoscape Apps - Replacement for Cytoscape
95. Try: http://chianti.ucsd.edu/~kono/dist/ Google Chrome Recommended!
96. Future Plan
97. Goals - Cytoscape as a service - Running on servers or clusters - Advanced analysis - Use Cytoscape as a part of workflow/pipeline - Handle huge networks (millions of edges) - Graph Database support - More integration to Cytoscape.js
98. Where to Start? - Cytoscape Web Site - cytoscape.org - Open Tutorials - opentutorials.cgl.ucsf.edu/ index.php/Main_Page
99. Getting Help - Two Google Groups - cytoscape-discuss@googlegroups.com - cytoscape-helpdesk@googlegroups.com - ANY question is OK!
101. www.cytoscape.org
102. 2013 Keiichiro Ono
     kono@ucsd.edu Slides will be available at: https://speakerdeck.com/keiono