Toolbox for including enzyme constraints on a genome-scale model.
Full Changelog: https://github.com/SysBioChalmers/GECKO/compare/v3.1.2...v3.1.3
makeEcModel
prevent duplicated protein pseudometabolitesapplyKcatConstraints
occassionally fills S-matrix with NaN in light ecModels (solves #344)calculateFfactor
handle data from PAXdb if the taxonomic ID is not 4 digits long (solves #345)runDLKcat
correctly handles param.path
if the folder name has spaces (solves #351)loadDatabases
throws error if duplicate protein IDs are foundgetSubsetEcModel
requires both bigEcModel
and smallGEM
to have derived from the same starting GEM, and will therefore check whether all reactions from smallGEM
are also present in bigEcModel
. (solves #353)HumanGEMAdapter.m
ecFSEOF
follow the original implementation of FSEOF (PR #356)startGECKOproject
addNewRxnsToEC
to add new enzyme-catalyzed metabolic reactions to an ecModel. (PR #337)readDLKcatOutput
reports which metabolites or reactions are not matching. (solves #334)mapRxnsToConv
throws error if empty flux vector is used as input. (solves #332)getComplexData
does not write empty complex data. (solves #338)Prot
to Enz
to give the new function names flexibilizeEnzConcs
, fillEnzConcs
and constraintEnzConcs
.ecFSEOF
as one combined function to run FSEOF simulations on ecModels.protocol.m
files.Features:
getComplexData
uses taxonomic ID instead of species name.GECKOInstaller
checks if correct RAVEN version is installed (release 2.8.3+).tutorials
, and userData
is removed as default location for model files. Users are encouraged to make their model folders outside the GECKO directory, facilitated by startGECKOproject()
.full_ecModel
tutorial:
plotCrabtree
makes plot that demonstrates Crabtree effect in ecModelsplotlightVSfull
makes plot comparing flux distribution in light and full ecModelslight_ecModel
:
getSubsetEcModel
ecFSEOF
is compatible with GECKO3.makeEcModel
can use pseudoRxns.tsv
to filter out pseudoreactions.reportEnzymeUsage
can make report of top-10 used enzymes.loadConventionalGEM
can load yaml
model files.enzymeUsage
reports as positive values.flexibilizeProtConcs
also keeps track of the ratio of protein concentration change.fillProtConcs
allows for selection of column from protData
, if it contains multiple datasets.setKcatForReactions
can directly modify a kcat for all associated reactions, useful for manual curation on existing ecModels.getReactionsFromEnzyme
gives which reactions are catalyzed by a particular enzyme, from a provided Uniprot ID.copyECtoGEM
to copy ecModel.ec.eccodes
to ecModel.eccodes
.Documentation:
/doc/
and online (becomes available upon PR commit).sensitivityTuning
allows for ignoring selected reactions.Fix / refactor:
protocol.m
(solves #279, #287).model.ec.concs
and proteomics data) are in mg/gDCW.getStandardKcat
can use data/pseudoRxns.tsv
as input of reactions to ignore, it overwrites previous standard Kcat definitions, and specifies model.ec.source{i} = 'standard'
if a standard kcat is assigned to a zero-kcat reaction (solves #280, #286)fuzzyKcatMatching
(solves #277), readDLKcatOutput
(solves #278), getECfromDatabase
(solves #281), sensitivityTuning
(solves #285), & applyCustomKcats
(solves #291).getECfromDatabase
incorrect definition of ecRxns and action input parameters.flexibilizeProtConcs
prevent infinite runs in no (more) proteins are limiting and check if protein pool is constraining growth.After significant refactoring of the codebase, GECKO 3 is more user-friendly, flexibile and versatile than before.
Most notable changes:
.ec
structure containing all enzyme and kcat information.userData
subfolder.modelAdapter
files contain parameters that are used in model reconstruction and analysis.matchKcats
and getEnzymesCodes
(PR #154)/geckomat/utilities/
(PR #119)./geckomat/utilities/
(PR #120).prot_abundance.txt
can now be an empty file (for organisms not present in pax-db) without the pipeline erroring (PR #124).generate_protModels.m
that constrained both the biomass and growth reactions (PR #107).version
for potential conflicts with Matlab (PR #113).