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OrganLists

This file contains lists of ograns as they are used in the whole-body metabolic model. Please note that the desired sex has to be specified (‘male’ or ‘female’)

Ines Thiele 2016 - 2017

addReactionsHH(model, rxnAbbrs, rxnNames, reactions, gprs, subSystems, couplingFactor)

This function add reaction(s) to the whole-body metabolic model, including the required coupling constraint. This function is based on model = addReaction(model,’newRxn1’,’A -> B + 2 C’)

[model] = addReactionsHH(model, rxnAbbrs,rxnNames, reactions, gprs, subSystems,couplingFactor)

INPUT model Model structure rxnAbbrs List of reaction abbreviation(s) to be added rxnNames List of reaction names reactions List of reaction formula {‘A -> B + 2 C’} gprs List of grRules subSystems List of subSystems couplingFactor Coupling factor to be added, default 20000

OUTPUT model Updated model structure

Ines Thiele 2018

loadPSCMfile(fileName, searchDirectory)

Loads a .mat file into the workspace, given a nickname or a full filename. If a nickname is given, i.e., “Harvey”, “Harvetta”, or Recon3D (legacy feature), the latest available version in the cobratoolbox is loaded. By specifiying the searchDirectory variable, .mat files are only searched in the given user defined directory. By default, all files within the MATLAB path variable are searched. If the full filename is given, the exact specified file is loaded.

USAGE

variable = loadPSCMfile (fileName, searchDirectory)

INPUTS: fileName: Nickname of .mat file to load or full name of .mat file to load

OPTIONAL INPUTS searchDirectory: User specified directory with .mat file to load.

OUTPUT: variable: Matlab variable returned

Example

% Giving only WBM nickname loads the latest available WBM: male = loadPSCMfile(‘Harvey’); % Giving the exact name of the .mat file loads the exact specified mode: female = loadPSCMfile(‘Harvetta_1_03d’); % Also specifiying the search directory loads the .mat file within that directory: male = loadPSCMfile(‘Harvetta’,’MYDIRECTORY’)

AUTHORS

• Ines Thiele, 2020

• Tim Hensen, July 2024: Removed hardcoding of WBMs names and added

option for searching a user defined directories.