GECKO

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readKcatTable: for loading curated kcat data

6

### Description of the new feature: Write a function (`readKcatTable`) that can load some standardized TSV file with manually curated kcat values, for instance derived from kmax determination. It should...

edkerk

In #170, the values from `model.ec.kcat` are used to include enzyme usage in the S-matrix. It can deal with both classic GECKO and GECKO light model formulations.

edkerk

refactor: update general kcat database

6

### Description of the new feature: By repurposing some of the DLKcat [code](https://github.com/SysBioChalmers/DLKcat/tree/master/DeeplearningApproach/Code/preprocess), construct a [JSON file](https://github.com/SysBioChalmers/DLKcat/tree/master/DeeplearningApproach/Data/database) similar as in DLKcat. This JSON contains kcat values from BRENDA and SABIO-RK...

edkerk

Add better support for multiple "base" models in the code by adding an Adapter pattern

7

We would create a base class called ModelAdapter that has functions such as "getParameters" and "getSpontaneousRxns". The GECKO code will then take an adapter (which is a class inheriting the...

johan-gson

### Description of the bug: I am using generate_protModels.m to integrate proteomics. Function description mention that ecModel_batch could be optional to speed-up the process. However, doing so without including it...

ae-tafur

### Description of the new feature: Instead of having GECKO's fuzzy matching approach directly modify the stoichiometric coefficients in the model, let it populate the `model.kcat` structure introduced in #156....

edkerk

Incorportate GECKO Light into the GECKO repo

1

GECKO Light does the following 1. Makes the model irreversible (same as original GECKO) 2. It penalizes each reaction with a protein cost that is MW/kcat 3. For complexes, the...

johan-gson

makeEcModel: model-specific kcat data in dedicated structure

5

### Description of the new feature: Instead of having kcat values only directly integrated as stoichiometric coefficients, keep a separate data structure with model-specific kcat values. Each field in the...

edkerk

Save auto-flexibilized enzymes during generate_protModels pipeline

3

### Description of the new feature: `flexibilizeProteins` is called from `constrainEnzymes` when generating proteome-constrained ecModels. In `flexibilizeProteins`, second round of flexibilization of abundances is carried out as part of `generate_protModels`...

alinarekena

### Description of the bug: When running constrainEnzymes on an existing ecModel (e.g. [ecYeastGEM.mat](https://github.com/SysBioChalmers/ecModels/blob/master/ecYeastGEM/model/ecYeastGEM.mat)) and with experimental data, the addRxns function from the RAVEN toolbox gives an error due to...

jdietrich3