🌱🍅 Multi-organs Plant Model 🍅🌱

Python project to do simulations on a genome-scale plant model with 3 organs (LEAF-STEM-ROOT) using FBA (CobraPy).

💡 Functionalities

• Generates organ-specific models from a generic plant model and FlexFlux contraints files,
• Runs sequencial FBA simulations, where:
  • The leaf tries to maximize its biomass rate, while exporting sucrose to sink organs,
  • Then, root and stem trie to minimize their sucrose uptake, while having to attain a fixed biomass rate (expressed as a fraction of the leaf's one)
• Stops the feedback loop and export output (plots, flux tables) when biomass rates converge.

📚 How to use

• Install the required dependencies:
  • Python 3.8(.10) (higher versions should work, but not tested yet),
  • CobraPy (pip install cobra),
  • PyYAML (pip install pyyaml),
  • Matplotlib for output plotting (pip install matplotlib).
• Inside the input directory, add input files (sbml, FlexFlux constraints) and edit config.yaml according to your needs.
• Run main.py.
• Results are written in the output directory.

🏗️ To-do List

• Logging,
• Docstrings,
• Better packaging, for use in another python project,
• Rewrite in OOP when possible (FlexfluxConstraints, OrganModel extends cobra.Model, ...),
• Optimize (may be hard considering the bottleneck that are the FBA themselves).