iPfal17 genome-scale metabolic reconstruction; lipid metabolism curation

Language: Python

Keywords: cobrapy, curation, genome-scale-models, malaria, python, systems-biology


This repository holds the iPfal17 genome-scale metabolic reconstruction with curated lipid metabolism and scripts that perform the curation and facilitate the model exploration. Additionally, there is a Python 3.5 virtual environment setup.

Usage of curation_script_cmd.py:

python curation_script_cmd.py -m data/plata_sbml_up_model.xml -d data/reaction_delete_edits_final.csv -e data/edits_additions_or_modifications_final.csv data/biomass_edits_final.csv

Usage of rxns_browser.py:

python rxns_browser.py -m <metabolite name> -mdl <model name>

for example:

python rxns_browser.py -m sphmyln160_c -mdl output/curated_model_2018_01_15_13\:13\:43.xml

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Michal Stolarczyk

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