Shameer-et-al-Role-of-mitochondria-in-C3-leaf-during-the-day

This repository contains scripts used to support our study the role of mitochondria in C3 leaves during the light-phase

Dependencies:

libsbml version 5.17.0
pandas version 0.23.4
cobrapy version 0.13.4

Instructions:

1. Install python version 2, libsbml, pandas and cobrapy
2. Go to folder contaning scripts
3. Open a console(max), terminal(linux) or command prompt(windows)
4. Run sripts (tw options available) ..a) using the command python scriptname.py where scriptname.py is the filename of the script

OR

        b) Enter python terminal using the command "python" and copy paste script contents to the python terminal

The latter method is recommended as it maintains the data in the python environment allowing one to analyse metabolic fluxes directly and make your own figures.

Index:

• Script1.py - estiamting curve used to calculate CO2 assimilation rate from photosynthetic photon flux density(PPFD) based on data from Donahue et al 1997
• Script1.ipynb - a jupyter notebok version of Script1.py
• Script2.py - generating Figure 3a
• Script2.ipynb - a jupyter notebok version of Script2.py
• Script3.py - generating Figure 3b
• Script3.ipynb - a jupyter notebok version of Script3.py
• Script4.py - generating data for Figure 4
• Script4.ipynb - a jupyter notebok version of Script4.py
• Script5.py - generating Figure 5a and 5b
• Script5.ipynb - a jupyter notebok version of Script5.py
• Script6.py - generating data for Figure 5c
• Script6.ipynb - a jupyter notebok version of Script6.py
• Script7.py - generating data for Figure 5d
• Script7.ipynb - a jupyter notebok version of Script7.py
• studyFunctions - a python module with functions used in scripts 1-7
• core_model.xml - a model representing primary metabolism in plant cells
• Gomes2015_Biomass.csv - a text file with Arabidopsis biomass composition gathered from Gomes et al 2015
• MetabolitesToTransfer.txt - a text file listing metabolites that will be allowed to accumulate over the diel cycle