PlantSimLab - a modeling and simulation web tool for plant biologists

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dc.contributor.authorHa, Sooken
dc.contributor.authorDimitrova, ‪Elenaen
dc.contributor.authorHoops, Stefanen
dc.contributor.authorAltarawy, Doaaen
dc.contributor.authorAnsariola, Mitraen
dc.contributor.authorDeb, Devduttaen
dc.contributor.authorGlazebrook, Janeen
dc.contributor.authorHillmer, Rachelen
dc.contributor.authorShahin, Hossameldin L.en
dc.contributor.authorKatagiri, Fumiakien
dc.contributor.authorMcDowell, John M.en
dc.contributor.authorMegraw, Mollyen
dc.contributor.authorSetubal, João C.en
dc.contributor.authorTyler, Brett M.en
dc.contributor.authorLaubenbacher, Reinhard C.en
dc.contributor.departmentFralin Life Sciences Instituteen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2019-10-28T12:04:23Zen
dc.date.available2019-10-28T12:04:23Zen
dc.date.issued2019-10-21en
dc.date.updated2019-10-27T08:29:37Zen
dc.description.abstractBackground At the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of experimental biology with mathematical modeling. One of the biggest challenges to making this integration a reality is that many life scientists do not possess the mathematical expertise needed to build and manipulate mathematical models well enough to use them as tools for hypothesis generation. Available modeling software packages often assume some modeling expertise. There is a need for software tools that are easy to use and intuitive for experimentalists. Results This paper introduces PlantSimLab, a web-based application developed to allow plant biologists to construct dynamic mathematical models of molecular networks, interrogate them in a manner similar to what is done in the laboratory, and use them as a tool for biological hypothesis generation. It is designed to be used by experimentalists, without direct assistance from mathematical modelers. Conclusions Mathematical modeling techniques are a useful tool for analyzing complex biological systems, and there is a need for accessible, efficient analysis tools within the biological community. PlantSimLab enables users to build, validate, and use intuitive qualitative dynamic computer models, with a graphical user interface that does not require mathematical modeling expertise. It makes analysis of complex models accessible to a larger community, as it is platform-independent and does not require extensive mathematical expertise.en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Bioinformatics. 2019 Oct 21;20(1):508en
dc.identifier.doihttps://doi.org/10.1186/s12859-019-3094-9en
dc.identifier.urihttp://hdl.handle.net/10919/95176en
dc.language.isoenen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderThe Author(s)en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titlePlantSimLab - a modeling and simulation web tool for plant biologistsen
dc.title.serialBMC Bioinformaticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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Journal Articles, BioMed Central and SpringerOpen
Scholarly Works, Fralin Life Sciences Institute
Scholarly Works, School of Plant and Environmental Sciences