README

Model Files:

reactions.yaml
- Reaction information for the model.

compounds.tsv
- Compound data for the model.

WP2-biomass.yaml
- Biomass and macromolecule synthesis reactions.

WP2-gene-associations.tsv
- Gene associations for reactions in the model.

WP2-Expression-TPM-table.tsv
- Tab separated table of TPM values for all genes in the WP2 genome based
on WP2 transcriptomes from growth at 4C, 15C, and 20C in late log phase.

model*.yaml
- Central model files for the overall WP2 model and each temperature based
model.

exchange/*
- Exchange files representing the LMO 812 media.

limits/*
- Flux limits settings for each temperature based model.

model-definitions/*
- Model definition files defining the reactions present in each of the
temperature based models.

tmfa-inputs/*
- Input files to run TMFA simulations on temperature based models.

GEM-iWP2.xml
- SBML version of the WP2 GEM. 

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Commands used to Run TMFA Simulations:

04 C Simulation:
psamm-model --model model-04C.yaml tmfa --temp 4 --config tmfa-inputs/config-04C.yaml simulation

15 C Simulation:
psamm-model --model model-15C.yaml tmfa --temp 15 --config tmfa-inputs/config-15C.yaml simulation

20 C Simulation:
psamm-model --model model-20C.yaml tmfa --temp 20 --config tmfa-inputs/config-20C.yaml simulation


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Analysis and Simulation Scripts
Each subfolder in the scripts/ directory contains pre-generated data files, and
the associated scripts needed to generate data summaries and figures.

pipeline/WP2-modeling.md
- Markdown file providing instructions on how to run all modeling scripts used
for simulation and analysis.

scripts/TMFA-Results/*
- Raw and summarized TMFA simulation data.

scripts/ATPM/*
- Scripts and data associated with ATP maintenance calculations.

scripts/efficiency/*
- Scripts associated with calculating metabolic efficiency metrics.

scripts/analysis/*
- Scripts associated with analysis of fluxes, deltaG values, concentrations, and
gene expression values.