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
network data integration, analysis, and visualization –Free! (Open source, LPGL) –Developed and maintained by universities, companies, and research institutions –Expandable by Apps/Plugins 6
- 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
- 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
- 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
- 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
• 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
for 3.x series Lille, June 17, 2013 Status of apps/plugins 31 3.0 Apps jActiveModules MCODE AgilentLiterature Search VennDiagramGenerator ClusterONE Centiscape GeneMANIA
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
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
Cytoscape Community – [email protected] – [email protected] – Tutorials & Manuals – Bug reports • Please cite us • Hope to see you all next fall • Questions: Welcome! 37
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