Input / output#

MATLAB functions in GECKO/src/io of the GECKO toolbox.

Functions#

Function

Summary

loadConventionalGEM

Load the conventional GEM (non-ecModel).

loadEcModel

Load the ecModel that matches the modelAdapter.

loadFluxData

Load total protein measurements and exchange flux data.

loadProtData

Load absolute proteomics data and average over replicates.

saveEcModel

Save an ecModel in YAML and/or SBML format.

Reference#

loadConventionalGEM#

function model = loadConventionalGEM(varargin)

Load the conventional GEM (non-ecModel).

Loads the conventional GEM (non-ecModel) from the location specified in the modelAdapter. By default, it looks in the models/ subdirectory of the param.path specified in the modelAdapter. When loading conventional GEMs from other locations, one can directly use importModel.

Name-Value Arguments

filename : char

name of the model file, without extension, located in the models/ subfolder of param.path as specified in the modelAdapter; it is loaded as SBML (.xml) (default: the value specified as param.convGEM in the modelAdapter, which may instead point to a YAML file).

modelAdapter : ModelAdapter

a loaded model adapter, from where the model folder is read (default: the current default model adapter).

Returns

model : struct

model in RAVEN format.

Examples

% optional arguments may be given positionally or as name-value pairs:
model = loadConventionalGEM(filename, modelAdapter);
model = loadConventionalGEM('filename', filename);

See also

loadEcModel

loadEcModel#

function model = loadEcModel(varargin)

Load the ecModel that matches the modelAdapter.

Loads the ecModel that matches the modelAdapter. By default, it loads the models/ecModel.yml in the directory specified as param.path in the modelAdapter. Alternative files in the same folder can be loaded by providing the appropriate filename. If loading models from other locations, one can directly use readYAMLmodel.

An ecModel whose protein usage and pool reactions run in the GECKO 3 direction is upgraded in the loaded model with upgradeEcModel, with a warning. An ecModel format (gecko_format in the file's metaData, see saveEcModel) above 4 is an error.

Name-Value Arguments

filename : char

name of the ecModel file (default 'ecModel.yml'). File should be located in the models/ subfolder of param.path as specified in the modelAdapter.

modelAdapter : ModelAdapter

a loaded model adapter, from where the model folder is read (default: the current default model adapter).

Returns

model : struct

an ecModel (with ecModel.ec structure).

Examples

% optional arguments may be given positionally or as name-value pairs:
model = loadEcModel(filename, modelAdapter);
model = loadEcModel('filename', filename);

See also

loadConventionalGEM, saveEcModel

loadFluxData#

function fluxData = loadFluxData(varargin)

Load total protein measurements and exchange flux data.

Loads total protein content and exchange flux data (e.g. carbon source, O2, CO2) from a tab-delimited file.

Name-Value Arguments

fluxDataFile : char

path to file with flux data (default reads data/fluxData.tsv as specified in modelAdapter).

modelAdapter : ModelAdapter

a loaded model adapter (default: the current default model adapter).

Returns

fluxData : struct

structure with flux data.

Notes

The fluxData structure has the following fields:

  • conds : sampling condition.

  • Ptot : total protein (g/gDCW).

  • grRate : growth rate (1/h).

  • exchFluxes : exchange fluxes (mmol/gDCWh).

  • exchMets : exchanged metabolites, matching exchFluxes.

  • exchRxnIDs : exchange reaction IDs, matching exchMets.

  • evotuneRMSEweight : if column existed in fluxData.tsv, weights for RMSE calculation in evotune kcat tuning.

  • source : if column existed in fluxData.tsv, description where the data comes from.

Examples

% optional arguments may be given positionally or as name-value pairs:
fluxData = loadFluxData(fluxDataFile, modelAdapter);
fluxData = loadFluxData('fluxDataFile', fluxDataFile);

See also

loadProtData

loadProtData#

function protData = loadProtData(replPerCond, varargin)

Load absolute proteomics data and average over replicates.

Loads absolute proteomics data (in mg/gDCW) and returns mean values across replicates for each condition in the data file. By default it also filters the data by various criteria, to remove uncertain data (see input parameters).

Parameters

replPerCond : double

vector with number of replicates for each condition in the dataset. Example: [3, 2] if first condition has triplicates and second condition has duplicates.

Name-Value Arguments

protDataFile : char

path to file with proteomics data, where protein levels are in mg/gDCW (default reads data/proteomics.tsv as specified in modelAdapter). Alternatively, protDataFile can be a protData structure that was previously made by loadProtData.

filterData : logical

whether abundances should be filtered. If false, minVal, maxRSD, maxMissing, cutLowest and addStdevs are not considered (default true).

modelAdapter : ModelAdapter

a loaded model adapter (default: the current default model adapter).

minVal : double

minimum mean protein measurement per condition; proteins with a lower mean abundance are discarded (set to NaN) for that condition (default 0, i.e. no lower threshold).

maxRSD : double

maximum relative standard deviation (RSD, the standard deviation across replicates divided by their mean) allowed per condition; proteins exceeding it are discarded (set to NaN) for that condition (default 1, i.e. RSD up to 100%).

maxMissing : double

minimum fraction of replicates within a condition that must have a measured value; proteins with fewer present replicates than this fraction requires are discarded (set to NaN) for that condition (default 2/3, i.e. at least two of three replicates must have a value). If conditions have different number of replicates (as indicated in replPerCond), maxMissing can also be a vector of the same length as replPerCond, with individual values per condition.

cutLowest : double

percentage of lowest mean values per condition to be discarded (not considering NaN values) (default 5).

addStdevs : double

how many standard deviations should be added to the mean value of each protein measurement across replicates, broadening the confidence interval (default 1).

Returns

protData : struct

structure with (filtered) proteome data.

Notes

The protData structure has the following fields:

  • uniprotIDs : cell array with Uniprot IDs matching protData.abundances.

  • abundances : matrix of proteomics data, where each column contains mean abundances per condition.

Examples

% optional arguments may be given positionally or as name-value pairs:
protData = loadProtData(replPerCond, protDataFile, filterData, modelAdapter, minVal, maxRSD, maxMissing, cutLowest, addStdevs);
protData = loadProtData(replPerCond, 'filterData', false);

See also

loadFluxData

saveEcModel#

function saveEcModel(ecModel,varargin)

Save an ecModel in YAML and/or SBML format.

Saves the ecModel in either YAML format (= default and preferred, as all ecModel content is reserved) and/or SBML format (= more widely compatible with other constraint-based modelling tools, can be used for running simulations like FBA etc., but this model cannot be loaded back into MATLAB for applying further GECKO functions, as model.ec is lost).

A YAML file records its ecModel format (gecko_format, see loadEcModel) and the GECKO release that wrote it (generator) in its metaData, in place of the geckopy_version that earlier geckopy releases wrote.

The ecModel is saved to the ecModel-specific models/ subfolder. For saving to other locations, writeYAMLmodel or exportModel are more suitable.

Parameters

ecModel : struct

an ecModel (with ecModel.ec structure).

Name-Value Arguments

filename : char

ending with either .yml or .xml, specifying if the ecModel should be saved in YAML or SBML file format. If no file extension is given, the ecModel will be saved in YAML format. If no filename is given, 'ecModel.yml' is used.

modelAdapter : ModelAdapter

a loaded model adapter, from where the model folder is read (default: the current default model adapter).

Examples

% optional arguments may be given positionally or as name-value pairs:
saveEcModel(ecModel,filename,modelAdapter);
saveEcModel(ecModel,'filename',filename);

See also

loadEcModel