Structural thermokinetic modelling for metabolic models

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Matlab code - getting started

Installation


  1. Matlab code for structural thermokinetic modelling can be downloaded from github
  2. Documentation of the code can be found here.
  3. Please note that some other matlab code (in particular, the Metabolic Network Toolbox for matlab, freely available on github) must be installed. Please see the installation instructions for further details.

Dependencies

The functions for structural thermokinetic modelling use data structures (e.g., for metabolic models) from the Metabolic Network Toolbox. To make full use of them, it may be good to become familiar with the functionality of the Metabolic Network Toolbox as well.

Getting acquainted with the workflow

After installing the toolbox, please have a look at the following demo scripts:

  1. stm/demo/demo_e_coli_glycolysis.m This script can be run interactively and shows how structural thermokinetic modelling and some additional analyses are applied to a metabolic model. The necessary input files (model in SBML format, graphics information in SBtab format) are loaded from the directory resources/models/demo_e_coli_glycolysis.
  2. elasticity_sampling_workflow.m This script contains alternative options for some of the steps in elasticity sampling. For example, the model can be loaded from different file formats (SBML, SBtab, .mat) Please modify it to adapt it your own models.

Running structural thermokinetic modelling with your own models

To apply structural thermokinetic modelling to your own models, you may provide them as SBML or Sbtab files, or build them within the Metabolic Network Toolbox. An important step in the workflow concerns the mapping of (metabolic and other) data to the model. To do this automatically, the workflow relies on comparable annotations or names between model and data. There are two possibilities: (i) Model and data can carry KEGG compound and reaction annotations. (ii) Data tables refer to the compound and reaction names used in the model.

Contact

If you have questions or other feedback, please contact me: Wolfram Liebermeister