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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. -------------- 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 -------------- 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.
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