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

Overview of the KETCHUP workflow divided into three different categories: i.) required user inputs, ii.) automated formulation of rate laws and incorporation of dataset, iii.) parameterization of kinetic model and stability check.

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

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