Reconstruction of the mathematical model of the photosynthetic electron transport chain using modelbase package
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README.MD
anoxia.py
instantiate.py
model.py
parameters.py
petc-modelbase-tutorial.ipynb
reactionrates.py
requirements.txt
runPAM.py

README.MD

Model of the photosynthetic electron transport chain

Model

This repository contains the mathematical model described in the paper published by Ebenhoeh et al. 2014, that has been originally developed in MATLAB. The model comprises a set of seven coupled ordinary differential equations and captures the temporal evolution of major protein complexes and key products of photosynthetic light reaction for model organism alga Chlamydomonas reinhardtii. The model has been written using modelbase package.

Install requirements

Sample analysis

A sample analysis is given in the accompanying notebook. We provide a set of prepared experimental protocols that can be easily amended by the user:

  • anoxia - simulates fluorescence trace in anoxia induced state transitions.
  • dld - simulates fluorescence trace in Dark-Light-Dark experiment.