GECKO
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SysBioChalmers
Toolbox for including enzyme constraints on a genome-scale model.
### Main improvements in this PR: As suggested in #171 - feat: - `findMetSmiles` function for querying PubChem for SMILES using metabolite names. - DLKcat in- and output files have...
Also adapted the code to be able to handle Human-GEM in addition to Yeast-GEM. I have not tested the code with Yeast-GEM. The code is not well tested at this...
### Description of the bug: Not able to retrieve data from UniProt via API #### Expected behavior: Download UniProt data #### Current behavior: Error using matlab.internal.webservices.HTTPConnector/copyContentToByteArray (line 396) The server...
#### Expected behavior: Mets in the basic model starting with conserved words such as 'prot_' should be detected at the beginning of makeEcModel and gives a warning. **I hereby confirm...
### Description of the new feature: I built two ecGEMs for my organism. One is reconstructed in a way that only contains genes id and the other is the BiGG...
### Main improvements in this PR: Solution to #160 Add two functions: 1. getComplexData.m to get curated information for complex in complex portal, and save it in a .json file....
### Description of the new feature: If the data is available, it could be taken into account that not all subunits are necessarily present in equal amounts in complexes. This...
### Description of the new feature: As based on #169, `runDLKcat`: - Gathers required information from the model, to be used as input for DLKcat. - Either directly runs DLKcat...
Currently, lossless export of ec-models can only be as .mat files, as SBML does not have fields to store many of the additional fields. The new `model.ec` structure would be...
Generally, EC codes are reaction specific, and can therefore be defined for each reaction. GECKO1/2 uses EC numbers to parse BRENDA, but this is currently extracted from a UniProt file....
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Toolbox for including enzyme constraints on a genome-scale model.