Releases: SysBioChalmers/GECKO
Releases · SysBioChalmers/GECKO
GECKO 3.1.3
- Fixes:
- resolve a bug when saving the ecModel in xml format #361
- Documentation:
- update DOI in code and Readme #362
- Features:
- clearer error message for use of Docker in Matlab #363
Full Changelog: v3.1.2...v3.1.3
GECKO 3.1.2
- Fixes:
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 handlesparam.path
if the folder name has spaces (solves #351)loadDatabases
throws error if duplicate protein IDs are foundgetSubsetEcModel
requires bothbigEcModel
andsmallGEM
to have derived from the same starting GEM, and will therefore check whether all reactions fromsmallGEM
are also present inbigEcModel
. (solves #353)
- Documentation:
- Installation instructions are moved to the Wiki
- Mention correct human-GEM version in
HumanGEMAdapter.m
- Replace Gitter with GitHub Discussions for asking support
- Refactor:
- Have
ecFSEOF
follow the original implementation of FSEOF (PR #356)
- Have
- Features:
- Navigate into new project folder after running
startGECKOproject
- Navigate into new project folder after running
GECKO 3.1.1
- Features:
- Fixes:
getComplexData
does not write empty complex data. (solves #338)
- Refactor:
- Rename
Prot
toEnz
to give the new function namesflexibilizeEnzConcs
,fillEnzConcs
andconstraintEnzConcs
. ecFSEOF
as one combined function to run FSEOF simulations on ecModels.
- Rename
- Documentation:
- Minor edits in
protocol.m
files.
- Minor edits in
GECKO 3.1.0
Main improvements in this PR:
-
Features:
- Renamed various parameters in model adapter.
getComplexData
uses taxonomic ID instead of species name.GECKOInstaller
checks if correct RAVEN version is installed (release 2.8.3+).- Tutorials are moved to
tutorials
, anduserData
is removed as default location for model files. Users are encouraged to make their model folders outside the GECKO directory, facilitated bystartGECKOproject()
. full_ecModel
tutorial:- more detailed discussions around kcat curation, protein usage etc.
plotCrabtree
makes plot that demonstrates Crabtree effect in ecModelsplotlightVSfull
makes plot comparing flux distribution in light and full ecModels
light_ecModel
:- minimum code to make a light ecModel based on human-GEM 1.15.0
- make contextualized ecModel based on a cell-line specific tINIT model with
getSubsetEcModel
ecFSEOF
is compatible with GECKO3.makeEcModel
can usepseudoRxns.tsv
to filter out pseudoreactions.- various functions show progress bar that indicates estimated remaining time.
reportEnzymeUsage
can make report of top-10 used enzymes.loadConventionalGEM
can loadyaml
model files.enzymeUsage
reports as positive values.flexibilizeProtConcs
also keeps track of the ratio of protein concentration change.fillProtConcs
allows for selection of column fromprotData
, 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 copyecModel.ec.eccodes
toecModel.eccodes
.
-
Documentation:
- All function documentation is available from
/doc/
and online (becomes available upon PR commit). sensitivityTuning
allows for ignoring selected reactions.
- All function documentation is available from
-
Fix / refactor:
- Numerous fixes and refactoring of code in many functions.
- Note that various functions have had their input parameters changed.
GECKO 3.0.2
- Documentation:
- Fix:
- Correct calculation of new protein pool if constrained with proteomics, by considering the total amount of measured protein.
getStandardKcat
can usedata/pseudoRxns.tsv
as input of reactions to ignore, it overwrites previous standard Kcat definitions, and specifiesmodel.ec.source{i} = 'standard'
if a standard kcat is assigned to a zero-kcat reaction (solves #280, #286)- Various bugfixes in
fuzzyKcatMatching
(solves #277),readDLKcatOutput
(solves #278),getECfromDatabase
(solves #281),sensitivityTuning
(solves #285), &applyCustomKcats
(solves #291).
GECKO 3.0.1
- Fix:
getECfromDatabase
incorrect definition of ecRxns and action input parameters.
- Features:
flexibilizeProtConcs
prevent infinite runs in no (more) proteins are limiting and check if protein pool is constraining growth.
- Documentation:
- Updated Issues and PR templates.
- Updated contributor guidelines.
- Updated README.md.
- Updated protocol.m.
- GitHub Pages.
GECKO 3.0.0
After significant refactoring of the codebase, GECKO 3 is more user-friendly, flexibile and versatile than before.
Most notable changes:
- ecModels have an
.ec
structure containing all enzyme and kcat information. - Enzymes are incorporated in the S-matrix as MW/kcat (previously this was 1/kcat, where the MW was instead considered in the protein exchange reactions).
- ecModels can be stored in YAML file format that retains all model content.
- The model-provided list of EC numbers can be used.
- Various kcat sources can easily be combined.
- DLKcat is distributed as part of GECKO, as alternative kcat source.
- Enzyme complex data can be gathered and considered.
- All model-specific files and scripts are kept in the
userData
subfolder. - Model-specific
modelAdapter
files contain parameters that are used in model reconstruction and analysis. - Because of the above, there is virtually no backwards compatibility with GECKO versions 1 and 2, regarding both models and code.
GECKO 2.0.3
- Refactor:
- speed improvements around
matchKcats
andgetEnzymesCodes
(PR #154)
- speed improvements around
GECKO 2.0.2
- Features:
- Fixes:
- Documentation/Styling/Others:
GECKO 2.0.1
- Fixes:
- UBs are only changed for strictly required proteins (PR #103).
- Closes #101: All yeast models in the toolbox are built on the same yeast-GEM version 8.1.3 (PR #105).
- Solved bug in
generate_protModels.m
that constrained both the biomass and growth reactions (PR #107). - Updated env. list after release of pandas 1.0 (PR #110).
- A folder for ecModels is added in case it doesn't exist already (PR #111).
- Closes #112: Avoid using the variable name
version
for potential conflicts with Matlab (PR #113).
- Style: