BIOL0044 MSci Investigaive Project for the Biological Sciences: Modelling Protometabolism

Code and reading materials related to my BIOL0044 MSci Investigative Project at the Lane Origins lab.

Project aims and outline

One of the aims of this investigative project is to implement a simple stochastic kinetic model of a plausible network of prebiotic metabolism. This is done using the GillespieSSA package in R, and this repo contains the majority of the resources used.

Repo structure and contents

Directories and some important contents:

• dependencies/ = contains snippets of abstracted and generalsied R scripts used to automate tasks e.g. plotting or state change matrix generation from .xlsx input
• bigger_pathway_materials/ = developing R code for a pipeline which starts with Stuart's curated materials (.xlsx), converting those to reactant and product names, generating a state-change matrix and propensity functions, etc.
  • bigger_network.Rmd = cleans Stuart's data file to yield lists of reactants, products, chemical reaction names, a state-change matrix and propensity functions etc based on bigger_pathway_rxns.xlsx(NB incomplete, check Notes section for more info)
  • big_st_ch_matrix.csv = first draft of the state-change matrix for the bigger simulation
  • big_pathway_sim_prep.RData = the data files needed to simulate the bigger network of reactions
• rev_c_fix/ = contains all files in relation to
  • archive/ = files with old notes, analyses, reports, etc
  • data/ = contains all .RData and .csv files used for analyses
  • images/ = contains all plots and visualisations created by .Rmd files in this directory
  • initial_prep/ = contains all EDA and initial readings
  • reversible_network[...].Rmd = the latest progress with introducing reversible reactions into the model; shows stages (working, debugging, etc)
  • network_visualisation.Rmd = rough draft of code visualising reversible C fixation network; nodes and edges are scaled; needs further abstraction at this stage
  • c_pathway_diagrams.pptx = simple diagrams of reversible C fixation

Individual files:

• bigger_pathway_rxns.xlsx = slightly modified file used to read pathways and reaction data in preparation for the simulation (see bigger_network.Rmd)
• bigger_pathway_rxns_original.xlsx = Stuart's manually curated protometabolic pathways of chemical reactions
• all_pathway_reactions_original.xlsx = larger network curated by Stuart; includes Wood-Ljungdhal; Krebs cycle; amino acid synthesis pathways...
• data_for_Stuart.zip = outputs from carbon fixation simulations (forward, reversible with negligble rate, reversible with equal rate)