Thesis

This repository contains files required to run and analyze a stoichiometric model of Marchantia polymorpha modified for the production of polyhydroxybutyrate (PHB), as explained in the thesis of Anya Lindström Battle, Department of Biology, University of Oxford

The files in this repository are as follows:

- FinalFunctions.ipynb: Jupyter notebook containing functions used to analyze the model

- Marchantia_PHB_model.xml: Final model of M. polymorpha metabolism used in this project, in SBML format.

- Cannell_et_al_Marchantia_model.xml: Model of M. polymorpha built by Cannell et al (2021) and used as a starting point in this project

- biomass_stoichiometry.xlsx: The biomass composition and component stoichiometry in the biomass equation, from Cannell et al (2021)

- met+rxns_added_to_model.xlsx: Reactions added to better represent metabolism of Marchantia, from Cannell et al (2021)

- PHB_reactions.csv: Reactions to add to the model to allow for the production of PHB

- transferMets.txt: A list of the transfer reactions to be added to the model

- DielOApattern.png: Data used for determination of carboxylic acid storage fluxes, generated by Corinna Hartinger, University of Oxford, UK

- WTvsCytosol_SignificantFluxDiff.csv and WTvsPlastid_SignificantFluxDiff.csv: Full list of reactions that differed between the baseline or cytosolic/plastidial PHB producing scenarios according to flux variability analysis.

#References: N. Cannell, University of Oxford, (2021).