SBMLmod: a Python-based web application and web service for efficient data integration and model simulation
Abstract Background 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 da...
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| Format: | Article |
| Language: | English |
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BMC
2017-06-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-017-1722-9 |
| _version_ | 1819145902658420736 |
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| author | Sascha Schäuble Anne-Kristin Stavrum Mathias Bockwoldt Pål Puntervoll Ines Heiland |
| author_facet | Sascha Schäuble Anne-Kristin Stavrum Mathias Bockwoldt Pål Puntervoll Ines Heiland |
| author_sort | Sascha Schäuble |
| collection | DOAJ |
| description | Abstract Background 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. 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. 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. |
| first_indexed | 2024-12-22T13:05:25Z |
| format | Article |
| id | doaj.art-0d4c87e177c84df49b4e40f6cafec41b |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-22T13:05:25Z |
| publishDate | 2017-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-0d4c87e177c84df49b4e40f6cafec41b2022-12-21T18:24:53ZengBMCBMC Bioinformatics1471-21052017-06-011811810.1186/s12859-017-1722-9SBMLmod: a Python-based web application and web service for efficient data integration and model simulationSascha Schäuble0Anne-Kristin Stavrum1Mathias Bockwoldt2Pål Puntervoll3Ines Heiland4Jena University Language & Information Engineering (JULIE) Lab, Friedrich-Schiller-University JenaDepartment of Informatics, University of BergenDepartment of Arctic and Marine Biology, UiT The Arctic University of NorwayCentre for Applied Biotechnology, Uni Research EnvironmentDepartment of Arctic and Marine Biology, UiT The Arctic University of NorwayAbstract Background 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. 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. 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.http://link.springer.com/article/10.1186/s12859-017-1722-9Web applicationWeb serviceData integrationModel simulation |
| spellingShingle | Sascha Schäuble Anne-Kristin Stavrum Mathias Bockwoldt Pål Puntervoll Ines Heiland SBMLmod: a Python-based web application and web service for efficient data integration and model simulation BMC Bioinformatics Web application Web service Data integration Model simulation |
| title | SBMLmod: a Python-based web application and web service for efficient data integration and model simulation |
| title_full | SBMLmod: a Python-based web application and web service for efficient data integration and model simulation |
| title_fullStr | SBMLmod: a Python-based web application and web service for efficient data integration and model simulation |
| title_full_unstemmed | SBMLmod: a Python-based web application and web service for efficient data integration and model simulation |
| title_short | SBMLmod: a Python-based web application and web service for efficient data integration and model simulation |
| title_sort | sbmlmod a python based web application and web service for efficient data integration and model simulation |
| topic | Web application Web service Data integration Model simulation |
| url | http://link.springer.com/article/10.1186/s12859-017-1722-9 |
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