KETCHUP: Parameterizing of Large-Scale Kinetic Models Using Multiple Datasets with Different Reference States
Themes: Conversion
Keywords: Metabolomics, Modeling
Citation
Hu, M., Suthers, P.F., Maranas, C.D. Feb. 7, 2024. “Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP)” GitHub Repository.
Overview
![](https://cabbi.bio/wp-content/uploads/2024/03/Maranas_KETCHUP_2024-jpg.webp)
Repository for Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP), a flexible parameter estimation tool that leverages a primal-dual interior-point algorithm to solve a nonlinear programming (NLP) problem that identifies a set of parameters capable of recapitulating the steady-state fluxes and concentrations in wild-type and perturbed metabolic networks.
KETCHUP can use K-FIT [2] input files. Example K-FIT input files are located in the K-FIT repository at https://github.com/maranasgroup/K-FIT.
Data
GitHub Repository: Includes code and updated installation guide.
Download (116.5 KB) includes:
- Model statistics
- Strain metabolites and fluxomics data
- Yield prediction comparisons