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README.md

MEWpy examples

This folder contains examples on how MEWpy can be used to perform phenotype simulations and Computational Strain Optimization.

Jupyter Notebooks:

  • The firs example, simulation, illustrates how MEWpy may be used to perform basic analysis tasks and phenotype simulations with GSMMs.

  • The second example, ROUProblem, illustrates how MEWpy may be used to identify reaction bounds modifications that favor the production of the aromatic amino acid (AAA) L-tyrosine in yeast.

  • The third example, GOUProblem, aims to increase the production of the same AAA in E. coli by modifying genes expression.

  • The last example, GeckoKOProblem, also targets the same goal in yeast by exploiting a GECKO model and by deleting enzymatic proteins.

Python scripts

  • load.py: Examples on how to load models and get a model specific phenotype simulator.
  • geneopt.py: Examples on how to run CSO thar modify genes expression.
  • gpr_eval.py: Examples om how to evaluate GPRs.
  • geckosimulation.py: Examples on how to run phenotype simulations on GECKO models.
  • cobra_geckoopt.py: Examples on how to run CSOs using the original GECKO model.
  • geckoopt.py: Examples on how to run CSOs using the original the REFRAME based GECKO model.
  • eacomparison.py: Compares the performance of distincts MOEAs on solving a GECKO OU problem.
  • smoment.py: Examples on how to run CSOs using sMOMENT and AUTOPACMEN GECKO like models for E.coli.
  • optram.py: OptRAM example.
  • rfba.py: rFBA example.
  • srfba.py: srFBA example.
  • optorf.py: OptORF examples.

More information can be found in the MEWpy documentation https://mewpy.readthedocs.io.