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README.md

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 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:
-  1) 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
+  1) A GEM model (Human1 or Human1-drived models). you can find Human1 model either in "inputs" folder or download it from here:
+     http://www.metabolicatlas.org/downloads/
   2) Uniprot ID of your interested protein.
   3) 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.
-  4) 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.
+  4) 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.
 
 After generating secModel maybe it can not produce your interested protein, in this case you can use secModelGapFilling function. This function will use a reference model to add reactions which could be used to fill gaps in secModel for protein production. This function will define a task for production of interested protein and use refrence model to satisfy the task.