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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 simulation and optimization notebooks, illustrate how MEWpy may be used to perform basic analysis tasks, phenotype simulations and optimizations using GSMMs.
  • The kinetic illustrates how MEWpy may be use to load and work with kinetic models.
  • The ROUProblem example 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 GOUProblem example aims to increase the production of the same AAA in E. coli by modifying genes expression.
  • The GeckoKOProblem, also targets the same goal in yeast by exploiting a GECKO model and by deleting enzymatic.
  • The CoFactorSwap illustrates how to swap co-factors to optimize the production of a metabolite.
  • The Community provides examples on how to use MEWpy to build community models.
  • The CrossFeeding illustrated how to use MEWpy to design strains that favor crossfeeding.
  • The GERM_Models example illustrates how to work with GERM models in MEWpy.
  • The GERM_Models_analysis example illustrates how to work with GERM models analysis in MEWpy. 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 on 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.
  • kinetic.py: Example on how to use MEWpy for strain design using a kinetic model.
  • optorf.py: OptORF examples.
  • optram.py: OptRAM example.
  • germ_models_analysis.py: Examples on how to perform GERM Model analysis in MEWpy.

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