title: REDEMPTION: reduced dimension ensemble modeling and parameter estimation.
abstract: 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.
  
  
  METHODS
  REDEMPTION can be downloaded from http://www.cabsel.ethz.ch/tools/redemption.
  
  
  BACKGROUND
  rudi.gunawan@chem.ethz.ch.
authors.affiliation: Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
authors.forename: Erica
authors.initials: E
authors.lastname: Manesso
authors.affiliation: Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
authors.forename: Rudiyanto
authors.initials: R
authors.lastname: Gunawan
mesh_terms: D000465:Algorithms; D008954:Models, Biological; D012984:Software