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JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations

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dc.contributor.authorPalmisano, Alidaen
dc.contributor.authorHoops, Stefanen
dc.contributor.authorWatson, Layne T.en
dc.contributor.authorJones, Thomas C.en
dc.contributor.authorTyson, John J.en
dc.contributor.authorShaffer, Clifford A.en
dc.contributor.departmentBiological Sciencesen
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentMathematicsen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.date.accessioned2016-12-09T21:43:42Zen
dc.date.available2016-12-09T21:43:42Zen
dc.date.issued2015-12-24en
dc.description.abstractBackground Most biomolecular reaction modeling tools allow users to build models with a single list of parameter values. However, a common scenario involves different parameterizations of the model to account for the results of related experiments, for example, to define the phenotypes for a variety of mutations (gene knockout, over expression, etc.) of a specific biochemical network. This scenario is not well supported by existing model editors, forcing the user to manually generate, store, and maintain many variations of the same model. Results We developed an extension to our modeling editor called the JigCell Run Manager (JC-RM). JC-RM allows the modeler to define a hierarchy of parameter values, simulations, and plot settings, and to save them together with the initial model. JC-RM supports generation of simulation plots, as well as export to COPASI and SBML (L3V1) for further analysis. Conclusions Developing a model with its initial list of parameter values is just the first step in modeling a biological system. Models are often parameterized in many different ways to account for mutations of the organism and/or for sets of related experiments performed on the organism. JC-RM offers two critical features: it supports the everyday management of a large model, complete with its parameterizations, and it facilitates sharing this information before and after publication. JC-RM allows the modeler to define a hierarchy of parameter values, simulation, and plot settings, and to maintain a relationship between this hierarchy and the initial model. JC-RM is implemented in Java and uses the COPASI API. JC-RM runs on all major operating systems, with minimal system requirements. Installers, source code, user manual, and examples can be found at the COPASI website (http://www.copasi.org/Projects).en
dc.description.versionPublished versionen
dc.format.extent? - ? (10) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Systems Biology. 2015 Dec 24;9(1):95en
dc.identifier.doihttps://doi.org/10.1186/s12918-015-0237-0en
dc.identifier.issn1752-0509en
dc.identifier.urihttp://hdl.handle.net/10919/73647en
dc.identifier.volume9en
dc.language.isoenen
dc.publisherBiomed Centralen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000367133500001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderPalmisano et al.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectMathematical & Computational Biologyen
dc.subjectSystems biologyen
dc.subjectBiological networksen
dc.subjectMathematical modelingen
dc.subjectChemical reaction systemsen
dc.subjectCOPASIen
dc.subjectSBMLen
dc.subjectSoftwareen
dc.subjectModel editoren
dc.subjectParameter hierarchyen
dc.subjectMutantsen
dc.subjectNETWORKSen
dc.subjectBUILDERen
dc.titleJigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizationsen
dc.title.serialBMC Systems Biologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineeringen
pubs.organisational-group/Virginia Tech/Engineering/COE T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineering/Computer Scienceen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen
pubs.organisational-group/Virginia Tech/Scienceen
pubs.organisational-group/Virginia Tech/Science/Biological Sciencesen
pubs.organisational-group/Virginia Tech/Science/COS T&R Facultyen
pubs.organisational-group/Virginia Tech/University Distinguished Professorsen
pubs.organisational-group/Virginia Tech/University Research Institutesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Biocomplexity Instituteen
pubs.organisational-group/Virginia Tech/University Research Institutes/Biocomplexity Institute/Researchersen

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