Multistate Model Builder (MSMB): a flexible editor for compact biochemical models

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dc.contributor.authorPalmisano, Alidaen
dc.contributor.authorHoops, Stefanen
dc.contributor.authorWatson, Layne T.en
dc.contributor.authorJones, Thomas C, Jr.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.accessioned2016-11-11T19:32:56Zen
dc.date.available2016-11-11T19:32:56Zen
dc.date.issued2014-04-04en
dc.description.abstractBackground Building models of molecular regulatory networks is challenging not just because of the intrinsic difficulty of describing complex biological processes. Writing a model is a creative effort that calls for more flexibility and interactive support than offered by many of today’s biochemical model editors. Our model editor MSMB -- Multistate Model Builder -- supports multistate models created using different modeling styles. Results MSMB provides two separate advances on existing network model editors. (1) A simple but powerful syntax is used to describe multistate species. This reduces the number of reactions needed to represent certain molecular systems, thereby reducing the complexity of model creation. (2) Extensive feedback is given during all stages of the model creation process on the existing state of the model. Users may activate error notifications of varying stringency on the fly, and use these messages as a guide toward a consistent, syntactically correct model. MSMB default values and behavior during model manipulation (e.g., when renaming or deleting an element) can be adapted to suit the modeler, thus supporting creativity rather than interfering with it. MSMB’s internal model representation allows saving a model with errors and inconsistencies (e.g., an undefined function argument; a syntactically malformed reaction). A consistent model can be exported to SBML or COPASI formats. We show the effectiveness of MSMB’s multistate syntax through models of the cell cycle and mRNA transcription. Conclusions Using multistate reactions reduces the number of reactions need to encode many biochemical network models. This reduces the cognitive load for a given model, thereby making it easier for modelers to build more complex models. The many interactive editing support features provided by MSMB make it easier for modelers to create syntactically valid models, thus speeding model creation. Complete information and the installation package can be found at http://www.copasi.org/SoftwareProjects. MSMB is based on Java and the COPASI API.en
dc.description.versionPublished versionen
dc.format.extent13 pagesen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Systems Biology. 2014 Apr 04;8(1):42en
dc.identifier.doihttps://doi.org/10.1186/1752-0509-8-42en
dc.identifier.issn1752-0509en
dc.identifier.urihttp://hdl.handle.net/10919/73423en
dc.identifier.volume8en
dc.language.isoenen
dc.publisherBiomed Centralen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000334805000001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderAlida Palmisano et al.; licensee BioMed Central Ltd.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.subjectMultistateen
dc.subjectNETWORKSen
dc.subjectSOFTWAREen
dc.titleMultistate Model Builder (MSMB): a flexible editor for compact biochemical modelsen
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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