COSMOS - COmmunity and Single Microbe Optimization System

COSMOS provides a computational framework for comparing monocultures and co-cultures in identical environments to identify the optimal microbial system. The analysis spans diverse environments, exploring factors such as medium composition, community interactions, and carbon sources.

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Key Scripts

• Masterscripts for Four Environments (effect of medium composition and oxygen availability):

  • aerobicRich.m
  • aerobicMinimal.m
  • anaerobicRich.m
  • anaerobicMinimal.m

  Initial inputs like models and parameters (environment and kinetic) can be changed by manipulating these files.

• Effect of Carbon Source:
  CSanalysis.m

  Masterscript for carbon source analysis in aerobic rich environment. Change the parameters for other environments as found in the above masterscripts.

• dynamic Flux Balance Analysis (dFBA):
  dFBACom.m

• Effect of Interactions:
  InteractionAnalysis.m

• Productivity Comparison:
  ProductivityAnalysis.m

• Yield Comparison:
  YieldAnalysis.m

  All the results in the paper are based on productivity comparison. Alternatively one can use yield comparison if required.

• Biomass Ratio Optimization:
  optBiomassRatio.m

• Experimental Validation:
  validation_SoKp.m

  To validate the algorithm by comparison with the experiments in https://doi.org/10.1186/s13068-023-02304-4

• Collating data from all four environments for statistical analysis:
  StatDataAnalysis.m and CS_StatDataAnalysis.m

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Models Used

All models were obtained from the BiGG Models and BioModels databases. Some annotations were adjusted to ensure consistent formatting across the dataset.

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Prerequisites

• MATLAB
• COBRA Toolbox
• IBM ILOG CPLEX

All simulations were conducted using MATLAB R2018a, COBRA Toolbox v3.0, and IBM ILOG CPLEX 12.8.

Please initialise the COBRA Toolbox and the solver before running COSMOS We recommend the ibm_cplex solver as COSMOS uses fastFVA for efficiency.

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How to Use

1. Clone the repository:

   git clone https://github.com/COSMOS.git