COMBINE 2016 Day 2: cy3sbml

COMBINE 2016

Matthias Koenig

Cytoscape is an open-source platform for visualizing networks. cy3sbml visualizes SBML information within the network context. It should visualize computational models and simulations which seamlessly integrate with computational modeling workflows and frameworks. cy3sbml is not a model builder, simulator or analysis tool. Accepted formats are SBML, OMEX, ResearchObjects, ODF, Cytoscape session files.You can import via file or URL, it has batch support and dedicated web services for BioModels.

In the networks, nodes correspond mainly to SBase objects and edges to the links between them. It works with models anywhere from small to genome-scale in size. There are multiple views (full networks, kinetic and base networks). They support annotations to retrieve information about respective SBMLOBject for each thing. The information can also be exported as RDF. There is also validation, and it produces a tabular validation report.

The data can be mapped to networks via node and edge attributes (eg via sid or metaid) and can be imported via CSV. Programmatic access is via the REST API via cyREST. It integrates with other applications, e.g. cy3sabiork for pulling kinetic information from SABIO-RK, and cyfluxviz for visualizations of FluxDistributions.

He then showed us a live demo.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

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