CAM-study-scripts

This repository contains scripts used to compare the energetics of CAM and C3 systems in fully developed leaves

Dependencies:

libsbml version 5.12.1
cobrapy version 0.5.4

Instructions:

1. Install python version 2, libsbml and cobrapy
2. Go to folder containing scripts
3. Open a console(mac), terminal(linux) or command prompt(windows)
4. Run scripts (two 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 - estimating non-growth associated maintenance (NGAM) in a fully developed C3 leaf
• Script2.py - modelling C3 and CAM systems: PPFD = 200 umol/m2/s
• Script3.py - modelling CAM in Opuntia ficus indica
• Script4.py - modelling C3 and CAM systems with fixed metabolic output
• Script5.py - comparing productivity of CAM and C3 systems
• Script6.py - comparing productivity of CAM and C3 systems with varying NGAM
• Script7.py - estimating NGAM in a fully developed C3 leaf in 18h6h day
• Script8.py - estimating NGAM in a fully developed C3 leaf in 6h18h day
• Script9.py - comparing productivity of CAM and C3 systems under different photoperiod conditions
• Script10.py - estimating NGAM in a fully developed C3 leaf when sugar:amino acids in the phloem = 0.5
• Script11.py - estimating NGAM in a fully developed C3 leaf when sugar:amino acids in the phloem = 0.7
• Script12.py - estimating NGAM in a fully developed C3 leaf when sugar:amino acids in the phloem = 0.99
• Script13.py - comparing productivity of CAM and C3 systems with varying sugar:amino acid ratio in the phloem
• Script14.py - estimating NGAM in a fully developed C3 leaf when day-night phloem export rate ratio is 3:2
• Script15.py - estimating NGAM in a fully developed C3 leaf when day-night phloem export rate ratio is 1:1
• Script16.py - comparing productivity of CAM and C3 systems with varying day-night phloem export rate ratio
• Script17.py - comparing productivity of fructan-storing CAM with symplastic and apoplastic loading
• diel_core_model - a model representing day and night time metabolism, that have yet to be configured for CAM or C3 metabolism
• C3_model - a model representing primary metabolism in C3 leaf with constraints matching that described in the paper
• CAM_model - a model representing primary metabolism in CAM leaf with constraints matching that described in the paper
• rxnpathwaydict - a file representing reactions and associated pathways which is required to print our pathway information in outputs
• pathwayprioritizer - a file listing pathways and a value for each pathway 1,2,3 ... which can be used to prioritize reactions in the output file for easy interpretation
• FractionalCharges - a file containing metabolite charges (to complement charge attribute in the model)
• MetabolitesToTransfer - a file listing metabolites that will be allowed to accumulate over the diel cycle
• VacuolarMetabolitesAtpH3DOT3 - a file listing metabolites that exists as fractional charges at pH=3.3
• OpuntiaBiomass - phloem composition reported in Opuntia ficus indica
• studyFunction - a python module with functions used in scripts 1-17
• core_model_4GA_20_10_17.xml - a proton balanced model of primary metabolism in plant cells