Io

OrganLists[source]

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, rxnNotes, rxnReferences)[source]

Add reaction(s) to the whole-body metabolic model with coupling constraints

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

USAGE:

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

INPUTS:

  • model – Whole-body metabolic model, with fields:

    • .rxns - reaction identifiers

    • .S - stoichiometric matrix

    • .A - constraint matrix (stoichiometry plus coupling constraints)

    • .subSystems - subsystem annotations

  • rxnAbbrs – List of reaction abbreviation(s) to add

  • rxnNames – List of reaction names

  • reactions – List of reaction formulae, e.g. {‘A -> B + 2 C’}

  • gprs – List of gene-protein-reaction rules

  • subSystems – List of subsystems

  • couplingFactor – Coupling factor to add (default 20000)

  • rxnNotes – List of notes for the reactions (optional)

  • rxnReferences – List of references for the reactions (optional)

OUTPUT:

model – Updated model structure

loadPSCMfile(fileName, searchDirectory)[source]

Load 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 COBRA Toolbox is loaded. By specifying searchDirectory, .mat files are only searched in that user defined directory; by default all files on the MATLAB path are searched. If the full filename is given, the exact specified file is loaded.

USAGE:

variable = loadPSCMfile (fileName, searchDirectory)

INPUTS:

fileName – Nickname of the .mat file to load, or the full name of the .mat file to load

OPTIONAL INPUTS:

searchDirectory – User specified directory with the .mat file to load

OUTPUT:

variable – MATLAB variable returned (the loaded model)

Example

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