cyanoRBA

A coarse-grained biochemical resource allocation model of phototrophic growth.

The framework is developed using Python 3.

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1. Getting python

You can download the latest version of Python here. Alternatively, you can use Anaconda to install python for your computer (Linux, Windows, Mac).

2. Installing packages using requirement file

  pip install -r requirements.txt

3. Installing the gurobi license

A detailed description of obtaining and installing Gurobi license is given here.

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Once you have checked the steps above. You may consider refering to the Beginners Guide. Or, just start a python console to simulate the RBA model of phototrophic growth.

4. To reproduce plots from the manuscript type the following in your python console:

run plot_results.py

5. To explore model capabilities:

run simulation.py

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A development version is hosted as a private git repository and people interested in contributing can request access by contacting the author (S.S.).