🌱🍅 Multi-organs Plant Model 🍅🌱

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

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.

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.

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).

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