Toolbox for generating protein-secretion genome-scale metabolic models based on Human GEM.
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 (Human1 or Human1-drived models) specialized to support protein secretory reactions. you can always find latest version of this model in input folder named as ihumanSec.
- Uniprot ID for your 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_v02.xlsx). You can call this list using importTempRxnsFromExcel.m function and then use output of this function in humanSec.m function.