Cytoscape 3.0: The evolution of an open-source network visualization tool and its new extensible architecture

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    The evolution of an open-source network visualization tool and its new extensible architecture Oriol Guitart Pla Systems Biology Lab Institut Pasteur Paris
2. Lille, June 17, 2013 Who am I? • Oriol Guitart Pla – Master in Electrical and Computer Science Engineering – Cytoscape Core Developer since March 2012 – Author of Cyni Toolbox App for Cytoscape 3.0 • Systems Biology Lab at Institut Pasteur – Develop novel concepts and tools for ‘omics data integration and network biology – Apply them to decipher complex biological processes – Examples: Dengue/bacterial infection, innate immunity, ... 2
3. Lille, June 17, 2013 You? • Your Background? – Biologists – Bioinformaticians – Mathematicians – Computer Scientists – Molecular Biogists – Other? • Your Cytoscape Experience? – First Time – 2.x Users – 3.0 Users – App/Plugin Developer 3
4. Lille, June 17, 2013 Outline • Introduction to Cytoscape • Cytoscape 3.0 • Apps/Plugins • Advanced topics 4
5. Lille, June 17, 2013 Introduction to Cytoscape • Overview • Core Concepts – Networks & Data Tables(Attributes) – Visual Mapping (VizMapper) – Apps/Plugins • Cytoscape Workflow • Working with Data – Import networks – Import data table (Attributes) • Cytoscape Tips & Tricks 5
6. Lille, June 17, 2013 Cytoscape •Open source platform for biological network data integration, analysis, and visualization –Free! (Open source, LPGL) –Developed and maintained by universities, companies, and research institutions –Expandable by Apps/Plugins 6
7. Lille, June 17, 2013 www.cytoscape.org 7
8. Lille, June 17, 2013 www.cytoscape.org 7 Toolbar
9. Lille, June 17, 2013 www.cytoscape.org 7 Network Views Toolbar
10. Lille, June 17, 2013 www.cytoscape.org 7 Network Panel Network Views Toolbar
11. Lille, June 17, 2013 www.cytoscape.org 7 Bird’s Eye View Network Panel Network Views Toolbar
12. Lille, June 17, 2013 www.cytoscape.org 7 Bird’s Eye View Network Panel Table Browser Network Views Toolbar
13. Annotated Network Lille, June 17, 2013 Core Concepts - Integration • Networks & Data Tables (Attributes) 8
14. Annotated Network Lille, June 17, 2013 Core Concepts - Integration • Networks & Data Tables (Attributes) 8
15. Annotated Network Lille, June 17, 2013 Core Concepts - Integration • Networks & Data Tables (Attributes) 8
16. Annotated Network Lille, June 17, 2013 Core Concepts - Integration • Networks & Data Tables (Attributes) 8
17. Annotated Network Lille, June 17, 2013 Core Concepts - Integration • Networks & Data Tables (Attributes) 8
18. • Visual Mapping (VizMapper) Lille, June 17, 2013 Core Concepts - Visualization 9
19. • Visual Mapping (VizMapper) Lille, June 17, 2013 Core Concepts - Visualization 9 Data Table
20. • Visual Mapping (VizMapper) Lille, June 17, 2013 Core Concepts - Visualization 9 Data Table VizMapper
21. • Visual Mapping (VizMapper) Lille, June 17, 2013 Core Concepts - Visualization 9 Data Table Use specific line types to indicate different types of interactions VizMapper
22. • Visual Mapping (VizMapper) Lille, June 17, 2013 Core Concepts - Visualization 9 Data Table Use specific line types to indicate different types of interactions Browse extremely dense networks by controlling for the opacity of nodes VizMapper
23. • Visual Mapping (VizMapper) Lille, June 17, 2013 Core Concepts - Visualization 9 Data Table Use specific line types to indicate different types of interactions Browse extremely dense networks by controlling for the opacity of nodes Expression data mapping VizMapper
24. • Visual Mapping (VizMapper) Lille, June 17, 2013 Core Concepts - Visualization 9 Data Table Use specific line types to indicate different types of interactions Browse extremely dense networks by controlling for the opacity of nodes Expression data mapping Set node sizes based on the degree of connectivity of the nodes VizMapper
25. • Visual Mapping (VizMapper) Lille, June 17, 2013 Core Concepts - Visualization 9 Data Table Use specific line types to indicate different types of interactions Browse extremely dense networks by controlling for the opacity of nodes Expression data mapping Set node sizes based on the degree of connectivity of the nodes Encode specific physical entities as different node shapes VizMapper
26. Lille, June 17, 2013 Core Concepts - Analysis • Apps/Plugins: Expanding Cytoscape Functionality 10
27. Show  the   results Cytoscape Workflow Lille, June 17, 2013 11 VizMapper Layouts Cytoscape   Apps Visualiza(on Computa(onal Analysis Human analysis Filtering Selec8on Data import Data export
28. Lille, June 17, 2013 Import Networks 12 • Network Data Formats – SIF – GML – XGMML – GraphML – BioPAX – PSI-MI – SBML – KGML(KEGG) – Excel – Delimited Text Table – CSV – Tab • Network DataBases – Protein - Protein – STRING - IntAct – Genetic – BioGRID – Protein - Compound – ChEMBL – Human-Curated Pathways – KEGG, Reactome, PathwayCommons
29. Lille, June 17, 2013 Import Data Table (Attributes) • Data Table: Any data that describes or provides details about nodes, edges, and networks • 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 13
30. Lille, June 17, 2013 Import Data Table (Attributes) • Data Table: Any data that describes or provides details about nodes, edges, and networks • 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 13 BRCA1
31. Lille, June 17, 2013 Import Data Table (Attributes) • Data Table: Any data that describes or provides details about nodes, edges, and networks • 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 13 BRCA1 GO Terms: DNA Repair Cell Cycle DNA Binding
32. Lille, June 17, 2013 Import Data Table (Attributes) • Data Table: Any data that describes or provides details about nodes, edges, and networks • 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 13 BRCA1 GO Terms: DNA Repair Cell Cycle DNA Binding NCBI Gene ID 672
33. Lille, June 17, 2013 Import Data Table (Attributes) • Data Table: Any data that describes or provides details about nodes, edges, and networks • 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 13 BRCA1 GO Terms: DNA Repair Cell Cycle DNA Binding NCBI Gene ID 672 On Chromosome 16
34. Lille, June 17, 2013 Import Data Table (Attributes) • Data Table: Any data that describes or provides details about nodes, edges, and networks • 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 13 BRCA1 GO Terms: DNA Repair Cell Cycle DNA Binding NCBI Gene ID 672 On Chromosome 16 Ensemble ID ENSG00000012048
35. Lille, June 17, 2013 Import Data Table (Attributes) • Data Table: Any data that describes or provides details about nodes, edges, and networks • 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 13 BRCA1 GO Terms: DNA Repair Cell Cycle DNA Binding NCBI Gene ID 672 On Chromosome 16 Ensemble ID ENSG00000012048 Public Data Sources
36. Lille, June 17, 2013 Cytoscape Tips & Tricks • When you open a large network, you will not get a view by default • Saving a session on a large screen may require some resizing when opened on your laptop • Cytoscape uses a lot of memory • An occasional restart when working with large networks is a good thing • Destroy views when you do not need them • Sometimes, if things get really messed up, deleting (or renaming) “.cytoscape” directory can give a clean state 14
37. Lille, June 17, 2013 Cytoscape 3.0 • Why a complete new version • Main differences with 2.x version • What’s new in 3.0 • Known issues • What next? 15
38. Lille, June 17, 2013 Why a complete new version? • 2.x done without explicit design guidelines or standards • API not well defined • Tightly coupled and interdependent (cyclic dependencies) • Hard to maintain and improve • Plugins could not share functionality 16
39. Lille, June 17, 2013 Main differences with 2.x • 3.0 almost completely rewritten • New modular architecture based on OSGi • Clear and simplified API • Implementation and API separated in different modules • RootNetwork/SubNetwork – Cytoscape 3 supports multiple root networks • Nodes and edges are shared within a single root network – Networks can have subnetworks • New concept of tables instead of attributes – CyRow and CyColumn interfaces 17
40. Lille, June 17, 2013 What’s new in 3.0 • New Welcome Screen 18
41. Lille, June 17, 2013 What’s new in 3.0 • Edge Bend Visual Property 19
42. Lille, June 17, 2013 What’s new in 3.0 • Edge Bundling 20
43. Lille, June 17, 2013 What’s new in 3.0 • Network Annotations – Add notes and simple shapes to background or foreground of a network view 21
44. Lille, June 17, 2013 What’s new in 3.0 • New Data Table Browser 22
45. Lille, June 17, 2013 What’s new in 3.0 • Network Collection – Cytoscape 3.0 manages networks based on network collections • Advanced Search Function – Search networks using Lucene syntax 23
46. Lille, June 17, 2013 Known Issues • Cytoscape 3 uses Java 6 or 7. Doesn’t work well on OpenJDK, better to use Oracle JRE/JDK • Cytoscape 2.x sessions work well in 3.0 but not the other way around • Windows XP with more than 1Gb of RAM might fail at the startup • Installation from zip or tar files with older versions installed, better to remove CytoscapeConfiguration folder 24
47. Lille, June 17, 2013 What next? • Possible 3.0.2 release in the next months if any important bug found • 3.1.0 release by the end of the year with several improvements: – Headless Mode ready – New Filtering UI – New VizMapper UI – Semantic zooming – New merge tool for data tables 25
48. Lille, June 17, 2013 Apps/Plugins • Overview • Simple Apps • Bundle Apps • The app Store • Status of Apps/Plugins • A 3.0 App exporting API (Cyni) 26
49. Lille, June 17, 2013 Cytoscape Apps/Plugins • Allow to extend cytoscape functionality • (Almost) all of them are free, so just play with it to learn what is possible • Lots of categories – Pathway Visualization – Data Import – Module Finding – ... • Apps, the new plugins – Cytoscape 3.0 has a new architecture so 2.x plugins are not longer valid – 3.0 new modular and standard architecture guarantee compatibility for all 3.x releases 27
50. Lille, June 17, 2013 Simple Apps • Inherit from a Class and get access to all cytoscape core functionality • Samples provided to help on development • Pros: – Easy. Very similar development approach than 2.x plugins – They do not require any understanding of OSGi • Cons: – Cannot take full advantage of new 3.0 architecture – Single Loader: Same problem than 2.x – No easy way to share functionality 28
51. Lille, June 17, 2013 Bundle Apps • OSGi based interface • A bundle is just a jar file along with a metadata file • Third party libraries can be included in the bundle • Many sample files also provided for development help • Pros: – Loaded independently. Your bundle can have different version of library than other bundles – Since you specifically register services, other apps can “get” those services • Cons: – More difficult development environment – If you export API, need to be careful with your API/ Implementation separation 29
52. Lille, June 17, 2013 The App Store • http://apps.cytoscape.org 30
53. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31
54. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31
55. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31
56. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31 3.0 Apps jActiveModules MCODE AgilentLiterature Search VennDiagramGenerator ClusterONE Centiscape GeneMANIA
57. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31
58. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31
59. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31 Integrated in 3.0 Core EnhancedSearch BiomartClient NetworkAnalyzer
60. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31
61. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31
62. • 140+ plugins for version 2.x series • 16 apps for 3.x series Lille, June 17, 2013 Status of apps/plugins 31 Plugins being ported ClusterMaker Genoscape MiMiplugin
63. Lille, June 17, 2013 Cyni Toolbox App • First 3.0 app that exports functionality • To biologists: – Cyni is a collection of tools for network inference • To bioinformaticians and inference researchers: – Cyni is a framework that supports and simplifies implementation of new network inference algorithms • Cyni provides – Several commonly used network inference techniques – Data imputation and discretization techniques – Several known metrics (correlation, bayesian,...) – Documented API – Tutorials and sample code 32
64. Lille, June 17, 2013 Cyni Use case 33
65. Lille, June 17, 2013 Cyni Use case 33 Infer a network from gene expression data
66. Lille, June 17, 2013 Cyni Use case 33
67. Load Data Lille, June 17, 2013 Cyni Use case 33
68. Load Data Lille, June 17, 2013 Cyni Use case 33 Estimate Data
69. Load Data Lille, June 17, 2013 Cyni Use case 33 Estimate Data Discretize Data
70. Load Data Lille, June 17, 2013 Cyni Use case 33 Estimate Data Discretize Data Infer Network
71. Lille, June 17, 2013 github.com/cytoscape 34
72. Lille, June 17, 2013 Cytoscape.js • JavaScript version of cytoscape for network visualization on the web browsers 35
73. Lille, June 17, 2013 Cytoscape Retreat 2013 • 9-11 October, Institut Pasteur, Paris – Symposium on Systems Biology (300 people Max) – App Expo Poster Session – Cytoscape User and Developer Tutorials (100 people Max) – http://nrnb.org/cyretreat/ 36
74. Lille, June 17, 2013 Thank you! • Getting help - Cytoscape Community – cytoscape-helpdesk@googlegroups.com – cytoscape-discuss@googlegroups.com – Tutorials & Manuals – Bug reports • Please cite us • Hope to see you all next fall • Questions: Welcome! 37