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README.md

Supplemental data for "Predicting metabolism during growth by osmotic cell expansion"

DOI:10.1101/731232

Scripts used in the study has been presented in Jupyter notebooks.

To run the scripts remotely without any installation, click on the binder icon below
Binder

Index

  • Script1.ipynb - Validating equations 3,4 and 5 used to estimate cellulose, phospholipid and protein content in expanding pericarp cells respectively (Figure 2).
  • Script2.ipynb - Modelling metabolism in dividing and expanding cells. (Figure 3)
  • Script3.ipynb - Processing data form Rontein et al 2002
  • Script4.ipynb - Fitting curves through experimentally determined fruit metabolite content using Colombie et al 2015 approach
  • Script5.ipynb - Developing constraints for phloem uptake rates during fruit development
  • Script6.ipynb - Step by step process of creating a multiphase developing fruit GrOE-FBA model (Figure 5,6,7 and Table 1)
  • Script7.ipynb - Script for Figure 5 and 7 (with FVA).
  • Script8.ipynb - Script for Figure 5 and 7 (without FVA for Binder).
  • Script9.ipynb - Script for Table 1
  • Script10.ipynb - Script for Figure 6
  • Data/Data_OrganicSolutes.csv - Experimentally determined organic solute content (per fruit)
  • studyFunctions.py - all custom functions used in this study
  • FractionalCharges.csv - a list of all metabolites (including their different charge states) and their charges
  • MetaboliteChargedStates.xlsx - an excel file containing information on the distribution of the different charge states of vacuolar metabolite across a wide range of pHs (data gathered using ChemAxon's pKa prediction tool)
  • MetaboliteTotransfer - the list of metabolites allowed to accumulate in the multiphase GrOE-FBA fruit model
  • Data/Data_Starch_Protein_original.csv - Experimentally determined starch and protein content (per gDW)
  • Data/Data_Starch_Protein.csv - Experimentally determined starch and protein content (per fruit)
  • Models/ConstrainedFruitModel.xml - a fully constrained version of the multiphase GrOE-FBA tomato fruit model
  • Models/FruitModel - a 10-phase version of the core model (PlantCoreMetabolism v1.2.3) with tomato GPR associations gathered from PlantCyc
  • Models/PlantCoreMetabolism_v1_2_3 - a charge balanced model of primary metabolism in plant tissues
  • processedData/ProcessedData_OrganicSolutes_Starch.csv - data generated by Script1.ipynb which is used in Script6.ipynb
  • processedData/default_ProcessedData_OrganicSolutes_Starch.csv - processed data set used to run Script6.ipynb in this study. The data set is presented here because Script1.ipynb involves random data subset generations which may result in difference in output files.

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Supplemental data for Shameer et al 2019 paper titled "Predicting metabolism during growth by osmotic cell expansion"

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