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Summary of Progress During the last 12 Months in the Standards Community

Summary of Progress During the last 12 Months in the Standards Community. Model Sharing Working Group Peter Hunter and Herbert M Sauro IMAG Meeting 2012. Standards for models, data & software. Experimental measurements. Minimum information standards: MIAME, MICEE,.

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Summary of Progress During the last 12 Months in the Standards Community

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  1. Summary of Progress During the last 12 Months in the Standards Community Model Sharing Working Group Peter Hunter and Herbert M Sauro IMAG Meeting 2012

  2. Standards for models, data & software Experimental measurements Minimum information standards: MIAME, MICEE, .. Data standards: DICOM, BioSignalML, .. Metadata:Ontologies Data repositories:PhysioNet, CAPdb, CVRG, .. APIs, webservices Validation,Limitations(Journal review) Metadata:Ontologies GO, FMA, .. Model standards: SBML, CellML, FieldML CurationAnnotation Need modules! Model repositories:Biomodels,PMR2 Referencedescription APIs, webservices Functional curation Simulation standards: SED-ML Software:OpenCOR, OpenCMISS, Continuity, Chaste, .. Verification, Benchmarks

  3. Progress in the SBML Standards World • The Composition/Modularity is now finalized and is supported by iBioSim (Myers) and Antimony (Lucian, Hucka, Sauro). This allows biochemical models to be modularized. • The Path2Models consortium project produced over 142,000 qualitative models translated from the KEGG Pathway database, using the draft SBML Level (http://code.google.com/p/path2models/) • The Level 3 Qualitative Modelspackage specification is almost to the release candidate stage, and is supported in JSBML and libSBML as well as at least 3 other software systems (Boolean networks, logical models and some petri-nets). • The Level 3 Flux Balance Constraintspackage definition has stabilized and the authors and considerable progress has been made on the specification document. It's supported in libSBML and will be in the upcoming JSBML 1.0. • The Level 3 Distribution & Rangespackage definition has had a lot of activity surrounding it, as it is an essential part of the European DDmore project. • Level 3 package documentationpages have be revamped • The SBML Test Suite has been updated with a lot more models (1123 now), especially to test Level 3, as well as enhance and reorganize the model metadata, and updated the online test system at sbml.org. • There has also been discussion on using SBML to support the exchange of PK/PD Models (See poster by James Sluka for more information). • New version of libSBMLreleased 5.6 • Etc…. • DDmore: Drug Disease Model Resources 

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