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Flux RETAP: A REaction Target Prioritization Genome-Scale Modeling Technique for Selecting Genetic Targets

A function for selecting reaction targets that have changes that are correlated/anti-correlated with product production.

Setup

Flux RETAP utilizes the cobra toolbox to perform simulations and has the following dependences:

  • cobra
  • scipy
  • pandas
  • numpy
  • matplotlib

If the required packages are not installed, you can use the following line from the command prompt to install:

pip install cobra scipy pandas numpy matplotlib

Instructions for use

To run Flux RETAP, download the FluxRETAP.py function and move it into the directory containing your code. The module can be imported the following command:

from FluxRETAP import FluxRETAP

Before simulation, it is necessary to import the cobra package and load the desired genome-scale model (see cobra documentation for more information) It is also necessary to supply FluxRETAP with:

  • product reaction name
  • carbon source reaction name
  • biomass reaction name
  • desired subsystems list (from the model)

A full tutorial demonstrating the parameters and use of FluxRETAP is provided here

Summary of files

  • core - directory containing main code of FluxRETAP and FluxRETAP functions
  • FluxRETAP_Tutorial.ipynb - notebook demonstrating how to use FluxRETAP
  • FluxRETAP_Results.ipynb - results reported in the manuscript comparing flux retap to other GSM techniques and experimental identified genes
  • Sensitivity.ipynb - sensitivity analysis of changing the parameters for heterologous indigoidine produciton in three different GSMs for Pseudomonas putida, Sacchromyces cerevisiae, and Escherichia coli

Reference

This project is not yet published

Copyright Notice

Flux REaction TArget Prioritization (Flux RETAP) Copyright (c) 2024, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected].

NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.

License

See license.txt for details.