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.

---

Key Scripts

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

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

• Effect of Interactions:
  InteractionAnalysis.m

• Effect of Carbon Source:
  CSanalysis.m

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

• Productivity Comparison:
  ProductivityAnalysis.m

• Yield Comparison:
  YieldAnalysis.m

• Biomass Ratio Optimization:
  optBiomassRatio.m

• Experimental Validation:
  validation_SoKp.m

---

Models Used

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

---

Prerequisites

• MATLAB
• COBRA Toolbox
• IBM ILOG CPLEX

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

We recommend the ibm_cplex solver as COSMOS uses fastFVA for efficiency.

---

How to Use

1. Clone the repository:

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