All code in this repository was used in the ODE-FBA leaf model study (paper details will be available here once the study is published)
Data : This folder contains biomass compositions and metabolic models used in the study
Data/biomass_soy.csv : Soy tissue specific biomass composition
Data/PlantCoreMetabolism_v2_0_0.xml : The PlantCoreMetabolism v2.0.0 model
Data/Soy_core_model_GA.sbml : PlantCoreMetabolism v2.0.0 with soy GRP associations
Data/GenerateSupplementalDataS2FromSoyModel.ipynb : A jupyter notebook adding Allantoin degradation pathway into Soy core model
Data/SupplementalDataS2.xml : SupplementalData S2
ePhotosynthesis : This folder contains all code required to run the ePhotosynthesis model in coupled and uncoupled configuration including the yaml files to run it via yggdrasil
ePhotosynthesis/InputEvn.txt : A text file for specifying light intensity, [CO2], daylength and whether sucrose export needs to be considered in the ODE model (leave as 1 when attempting to replicate results in the study)
ePhotosynthesis/InputATPCost.txt : A text file for specifying Vatp_ode
ePhotosynthesis/InputNADPHCost.txt : A text file for specifying Vnadph_ode
ePhotosynthesis/Sim_Ephotosynthesis.m : M file to run ephotosynthesis model
ePhotosynthesis/EphotosynthesisOnly.yml : YAML file to run ephotosynthesis model via yggdrasil
ePhotosynthesis/OutputFluxT.txt: A text file containing results of an ODE model run
ePhotosynthesis/FluxAnnotation.xlsx: An excel file containing annotations for the ODE outputs
FBA : This folder contains all code required to run the FBA model in coupled and uncoupled configuration including the yaml files to run it via yggdrasil
FBA/dielFBA_model_only.py : Python code to run the diel FBA model on its own (a.k.a FBA model in text)
FBA/yggrasil_ODE_FBA_dielFBA_only.yaml : YAML file to run FBA model via yggdrasil
FBA/dielFBA_model_forODE.py : Python code to run diel FBA model in LC configuration
FBA/yggrasil_ODE_FBA_dielFBA.yml : YAML file to run LC model via yggdrasil
FBA/FBA_model_for_ODE.py : Python code to run FBA module representing day-time metabolism in TC configuration
FBA/yggrasil_ODE_FBA_testing.yaml : YAML file to run day-time FBA module of TC via yggdrasil
FBA/FBA_model_for_ODE_night.py : Python code to run FBA module representing night-time metabolism in TC configuration
FBA/yggrasil_ODE_FBA_night.yaml : YAML file to run night-time FBA module of TC via yggdrasil
FBA/FBA_model_growing_forODE.py : Python code to run FBA module representing growing leaf day-time metabolism in TC configuration
FBA/yggrasil_ODE_FBA_growing.yaml : YAML file to run day-time growing leaf FBA module via yggdrasil
FBA/FBA_model_growing_forODE.py : Python code to run FBA module representing growing leaf night-time metabolism in TC configuration
FBA/yggrasil_ODE_FBA_night_growing.yaml : YAML file to run night-time growing leaf FBA module via yggdrasil
FluxMap : This folder contains SVG/PNG files of flux maps used in the paper and code used to study fluxes
FVA : Folder containing jupyter notebook demonstrating how we managed to ensure unique flux values through NTT during pFBA
sensitivityAnalyses : Folder contains all code, results and final compilations associated with testing model sensitivity to FBA parameters
sensitivityAnalyses/NGAM : Folder contains all code, results and final compilations associated with testing model sensitivity to non-growth associated maintenance cost
sensitivityAnalyses/phloemComposition : Folder contains all code, results and final compilations associated with testing model sensitivity to phloem composition using data collected from Wilkinson and Douglas 2003
sensitivityAnalyses/starchOAAratios : Folder contains all code, results and final compilations associated with testing model sensitivity to organic acid accumulation/remobilization constraint (equation 5 and 6)
Analysis : Folder containing code, log, results and final compilation of results associated with studying metabolism in leaves under varying PPFD and [CO2] using TC
Validations : Folder containing code, logs, results and final compilation of results associated with Figures 3,4,5 and 7, and Tables 1 and 2
Validations/ODE_Figure2A.py : code used to run ODE model for Figure 3A
Validations/LC_Figure2A.py : code used to run LC model for Figure 3A
Validations/TC_Figure2A.py : code used to run TC model for Figure 3A
Validations/FBA_Figure2B.py : code used to run TC model for Figure 3B
Validations/ODE_Figure2B.py : code used to run ODE model for Figure 3B
Validations/LC_Figure2B.py : code used to run LC model for Figure 3B
Validations/TC_Figure2B.py : code used to run TC model for Figure 3B
Validations/Script1.ipynb : jupyter notebook code to generate Figure 3A
Validations/Script2.ipynb : jupyter notebook code to generate Figure 3B
Validations/YggdrasilLooping_LooselyCoupledFACE.py : Python code to model FACE conditions with LC model using yggdrasil
Validations/YggdrasilLooping.py : Python code to model mature leaf metabolism using TC model via yggdrasil
Validations/YggdrasilLooping_growing.py : Python code to model growing leaf metabolism using TC model via yggdrasil
Validations/YggdrasilLooping_FACE%_372.py : Python code to model leaf metabolism on day % of FACE experiment under ambient CO2 conditions using TC model
Validations/YggdrasilLooping_FACE%_552.py : Python code to model leaf metabolism on day % of FACE experiment under elevated CO2 conditions using TC model