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Toolbox for generating protein-secretion genome-scale model for Human.

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Name		Name	Last commit message	Last commit date
Latest commit History 30 Commits
inputs		inputs
README.md		README.md
addCanonicalRxns.m		addCanonicalRxns.m
addCompartmentalizedMetNames.m		addCompartmentalizedMetNames.m
addPathway.m		addPathway.m
addPathwayFromCondition.m		addPathwayFromCondition.m
findConnectorMets.m		findConnectorMets.m
getCompsFromRxnNames.m		getCompsFromRxnNames.m
getGPRsFromRxnNames.m		getGPRsFromRxnNames.m
humanSec.m		humanSec.m
importPsimFromExcel.m		importPsimFromExcel.m
importTempRxnsFromExcel.m		importTempRxnsFromExcel.m
insert_prot_name_in_rxnFormula.m		insert_prot_name_in_rxnFormula.m
insert_prot_name_in_rxnName.m		insert_prot_name_in_rxnName.m
optimizeSecModel.m		optimizeSecModel.m
splitComp.m		splitComp.m
substitute_AAs_count.m		substitute_AAs_count.m
translationRxn.m		translationRxn.m

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HumanSec

Toolbox for generating protein-secretion genome-scale model for Human.

To test this toolbox and generate a protein-specific genome-scale model you just need to run humanSec.m function. This function needs following inputs:

A GEM model (HMR2 or HMR2-drived models). you can find hmr2 model either in "inputs" folder or download it from here: http://www.metabolicatlas.org/downloads/hmr
Uniprot ID of your interested protein.
Protein-Specific Information Matrix (there is a list of human proteins in excel format in "inputs" folder named PSIM_HUMAN.xlsx). You can call this list using importPsimFromExcel.m function and then use output of this function in humanSec.m function.
List of template reactions (there is a list of template reactions in excel format in "inputs" folder named tempRxns_v01.xlsx). You can call this list using importTempRxnsFromExcel.m function and then use output of this function in humanSec.m function.