SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments
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Nim-2013-SPEDRE_ a web server.pdf
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Author(s)
Nim, Tri Hieu
White, Jacob K.
Tucker-Kellogg, Lisa
Date Issued
June 2013
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
Nim, T. H., J. K. White, and L. Tucker-Kellogg. “SPEDRE: a Web Server for Estimating Rate Parameters for Cell Signaling Dynamics in Data-rich Environments.” Nucleic Acids Research 41.W1 (2013): W187–W191.
Version
Final published version
Abstract
Cell 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.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Singapore-MIT Alliance in Research and Technology (SMART)
Terms of Use
Creative Commons Attribution Non-Commercial
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1093/nar/gkt459
