General Information
| Description | Reduced dimension ensemble modeling and parameter estimation |
| Homepage | http://www.cabsel.ethz.ch/tools/redemption |
Publications
REDEMPTION: reduced dimension ensemble modeling and parameter estimation
Summary:
Here, we present REDEMPTION (duced imension nsemble odeling and arameter estima), 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
Related Tools
GenSSI
Published July 2011
A software toolbox for structural identifiability analysis of biological models
SBML-PET-MPI
Published February 2011
A parallel parameter estimation tool for Systems Biology Markup Language based models
OKVAR-Boost
Published April 2013
A novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks
SEK
Published May 2014
Sparsity exploiting k-mer-based estimation of bacterial community composition
Data2Dynamics
Published July 2015
A modeling environment tailored to parameter estimation in dynamical systems
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
