The package qmut contains mainly a class called QuantitativeMutation to enable the simulation of quantitative mutations of whole genome metabolic reconstructions.
- Check that you have
cobrapyinstalled in your environment - Download and copy the
\cobrapy_qmutfolder in your working directory, or - Download and run
pip install path_to_setup.py_parent_folder
In this tutorial we will show the main applications and methods of the QuantiativeMutation objects, briefly:
- Load a metabolic model and create its QuantitativeMutation object
- Using
Q.optimize()andQ.slim_optimize()to find solutions and biomass production rate, respectively. - Generating random media following the protocol of Wang and Zhang and applying it to
Q. - Compute maximal bounds of
Qacross a list of media. And save/load them withQ.load_bounds()andQ.save_bounds() - Check how gene reaction rules are quantitatively interpreted.
- Working with relative gene dosages and quantitative mutations.
- Compute individuals, and populations in a single or in multiple processors.
If you find this class useful and you use it in your work, please also cite its paper: The limitations of phenotype prediction in metabolism, Pablo Yubero, Alvar A. Lavin, Juan F. Poyatos bioRxiv 2022.05.19.492732; doi: https://doi.org/10.1101/2022.05.19.492732
If your have any issue with this repo please contact me through github rather than email. Feel free to ask for updated versions of it as perhaps I miss to keep this repo up to date.