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dc.contributor.authorSchäuble, Sascha
dc.contributor.authorStavrum, Anne-Kristin
dc.contributor.authorBockwoldt, Mathias
dc.contributor.authorPuntervoll, Pål
dc.contributor.authorHeiland, Ines
dc.date.accessioned2018-01-09T08:45:45Z
dc.date.available2018-01-09T08:45:45Z
dc.date.issued2017-06-24
dc.description.abstractBACKGROUND: Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. <br>RESULTS: We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models. Subsequent steady state analysis is readily accessible via the web service COPASIWS. We illustrate the utility of SBMLmod by integrating gene expression data from different healthy tissues as well as from a cancer dataset into a previously published model of mammalian tryptophan metabolism. <br>CONCLUSION: SBMLmod is a user-friendly platform for model modification and simulation. The web application is available at http://sbmlmod.uit.no , whereas the WSDL definition file for the web service is accessible via http://sbmlmod.uit.no/SBMLmod.wsdl . Furthermore, the entire package can be downloaded from https://github.com/MolecularBioinformatics/sbml-mod-ws . We envision that SBMLmod will make automated model modification and simulation available to a broader research community.en_US
dc.descriptionSource at <a href=https://doi.org/10.1186/s12859-017-1722-9> https://doi.org/10.1186/s12859-017-1722-9 </a>en_US
dc.identifier.citationSchäuble S, Stavrum A, Bockwoldt M, Puntervoll P, Heiland I. SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. BMC Bioinformatics. 2017;18(314):1-8en_US
dc.identifier.cristinIDFRIDAID 1488197
dc.identifier.doi10.1186/s12859-017-1722-9
dc.identifier.issn1471-2105
dc.identifier.urihttps://hdl.handle.net/10037/11937
dc.language.isoengen_US
dc.publisherBioMed Centralen_US
dc.relation.journalBMC Bioinformatics
dc.relation.projectIDNorges forskningsråd: 178885en_US
dc.relation.projectIDAndre: BMBF e:Med GlioPATHen_US
dc.relation.projectIDAndre: DAAD-exchange programen_US
dc.relation.projectIDinfo:eu-repo/grantAgreement/RCN/EVITA/178885/NORWAY/eSysbio - an e-science environment for systems biology//en_US
dc.rights.accessRightsopenAccessen_US
dc.subjectVDP::Matematikk og Naturvitenskap: 400::Informasjons- og kommunikasjonsvitenskap: 420::Simulering, visualisering, signalbehandling, bildeanalyse: 429en_US
dc.subjectVDP::Mathematics and natural science: 400::Information and communication science: 420::Simulation, visualization, signal processing, image processing: 429en_US
dc.titleSBMLmod: a Python-based web application and web service for efficient data integration and model simulationen_US
dc.typeJournal articleen_US
dc.typeTidsskriftartikkelen_US
dc.typePeer revieweden_US


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