Please use this identifier to cite or link to this item: https://doi.org/10.1093/nar/gkt459
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dc.titleSPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments.
dc.contributor.authorNim, T.H.
dc.contributor.authorWhite, J.K.
dc.contributor.authorTucker-Kellogg, L.
dc.date.accessioned2016-06-02T10:29:43Z
dc.date.available2016-06-02T10:29:43Z
dc.date.issued2013-07
dc.identifier.citationNim, T.H., White, J.K., Tucker-Kellogg, L. (2013-07). SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments.. Nucleic acids research 41 (Web Server issue) : W187-191. ScholarBank@NUS Repository. https://doi.org/10.1093/nar/gkt459
dc.identifier.issn13624962
dc.identifier.urihttp://scholarbank.nus.edu.sg/handle/10635/125010
dc.description.abstractCell signaling pathways and metabolic networks are often modeled using ordinary differential equations (ODEs) to represent the production/consumption of molecular species over time. Regardless whether a model is built de novo or adapted from previous models, there is a need to estimate kinetic rate constants based on time-series experimental measurements of molecular abundance. For data-rich cases such as proteomic measurements of all species, spline-based parameter estimation algorithms have been developed to avoid solving all the ODEs explicitly. We report the development of a web server for a spline-based method. Systematic Parameter Estimation for Data-Rich Environments (SPEDRE) estimates reaction rates for biochemical networks. As input, it takes the connectivity of the network and the concentrations of the molecular species at discrete time points. SPEDRE is intended for large sparse networks, such as signaling cascades with many proteins but few reactions per protein. If data are available for all species in the network, it provides global coverage of the parameter space, at low resolution and with approximate accuracy. The output is an optimized value for each reaction rate parameter, accompanied by a range and bin plot. SPEDRE uses tools from COPASI for pre-processing and post-processing. SPEDRE is a free service at http://LTKLab.org/SPEDRE.
dc.sourceScopus
dc.typeArticle
dc.contributor.departmentBIOLOGICAL SCIENCES
dc.description.doi10.1093/nar/gkt459
dc.description.sourcetitleNucleic acids research
dc.description.volume41
dc.description.issueWeb Server issue
dc.description.pageW187-191
dc.identifier.isiut000323603200030
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