REDEMPTION: reduced dimension ensemble modeling and parameter estimation.
- Liu Y Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- Manesso E Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- Gunawan R Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- 2015-06-17
Published in:
- Bioinformatics (Oxford, England). - 2015
English
UNLABELLED
Here, we present REDEMPTION ( RE: duced D: imension E: nsemble M: odeling and P: arameter estima TION: ), a toolbox for parameter estimation and ensemble modeling of ordinary differential equations (ODEs) using time-series data. For models with more reactions than measured species, a common scenario in biological modeling, the parameter estimation is formulated as a nested optimization problem based on incremental parameter estimation strategy. REDEMPTION also includes a tool for the identification of an ensemble of parameter combinations that provide satisfactory goodness-of-fit to the data. The functionalities of REDEMPTION are accessible through a MATLAB user interface (UI), as well as through programming script. For computational speed-up, REDEMPTION provides a numerical parallelization option using MATLAB Parallel Computing toolbox.
AVAILABILITY AND IMPLEMENTATION
REDEMPTION can be downloaded from http://www.cabsel.ethz.ch/tools/redemption.
CONTACT
rudi.gunawan@chem.ethz.ch.
Here, we present REDEMPTION ( RE: duced D: imension E: nsemble M: odeling and P: arameter estima TION: ), a toolbox for parameter estimation and ensemble modeling of ordinary differential equations (ODEs) using time-series data. For models with more reactions than measured species, a common scenario in biological modeling, the parameter estimation is formulated as a nested optimization problem based on incremental parameter estimation strategy. REDEMPTION also includes a tool for the identification of an ensemble of parameter combinations that provide satisfactory goodness-of-fit to the data. The functionalities of REDEMPTION are accessible through a MATLAB user interface (UI), as well as through programming script. For computational speed-up, REDEMPTION provides a numerical parallelization option using MATLAB Parallel Computing toolbox.
AVAILABILITY AND IMPLEMENTATION
REDEMPTION can be downloaded from http://www.cabsel.ethz.ch/tools/redemption.
CONTACT
rudi.gunawan@chem.ethz.ch.
- Language
-
- English
- Open access status
- hybrid
- Identifiers
-
- DOI 10.1093/bioinformatics/btv365
- PMID 26076722
- Persistent URL
- https://sonar.ch/global/documents/40893
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