GECKO

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Having a poke around [updateDatabases.m](https://github.com/SysBioChalmers/GECKO/blob/devel/geckomat/get_enzyme_data/updateDatabases.m), I see a potential improvement around how the KEGG API is used: https://github.com/SysBioChalmers/GECKO/blob/6fbc627ca07cf7637cd0a95355ed1e1e1c2ee1f0/geckomat/get_enzyme_data/updateDatabases.m#L71-L92 Currently, as far as I understand, the process is to get a...

mihai-sysbio

bug: very low fluxes, close to solver tolerance

4

### Description of the bug: The units by which enzymes are incorporated (mmol and g/gDCW) results in low stoichiometric coefficients, low UB for protein exchange reactions constrained by proteomics measurements,...

edkerk

### Description of the new feature: In `fermentationData.txt` (as in `chemostatData.tsv`) the fluxes are all positive, while the column names indicate whether something is uptake or secretion. In essence this...

edkerk

Some hard-coded parameters could be moved out of the `fitGAM` function, to make the code more versatile, and so no custom function edits would be required if a model would...

edkerk

feat: allow non-default GAM parameters

1

Addresses #133: - `getModelParameters` contains the optional `parameters.maxGAM`, which can be used to specify the scanned GAM range (GAM = 20:5:100) in `fitGAM`. If not specified, a maximum GAM of...

edkerk

feat: specify carbon source with fermentation data

2

When generating multiple proteomics-constrained ec-models with different carbon sources, this currently would require different `getModelParameters.m` and `fermentationData.txt` files. Instead, in this PR: - the carbon source exchange reaction name is...

edkerk

As noticed in PR #128, the predicted max. growth rate for the `ecYeastGEM` growing on glucose minimal media does not correspond to the provided experimental value in `getModelParameters`. Actually, the...

IVANDOMENZAIN

### Main improvements in this PR: **I hereby confirm that I have:** - [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/GECKO) for running GECKO - [ ] Selected `devel` as...

IVANDOMENZAIN

feat: met/rxn metadata in ecModels

1

As mentioned in https://github.com/SysBioChalmers/GECKO/pull/125, currently we are stripping off most metadata associated to reactions and metabolites from ecModels, including metabolite charges, reaction EC numbers, ChEBI/KEGG ids, etc. This was originally...

BenjaSanchez

Information on how accurately the Kcat-values extracted from BRENDA is matched to the chosen organism is important metadata. While it is possible to get this information by running run lines...

sulheim