GECKO
GECKO copied to clipboard
SysBioChalmers
Toolbox for including enzyme constraints on a genome-scale model.
BRENDA now includes EC main class 7 for distinguishing transport reactions (i.e. EC7.x.x.x), so some automatic/manual search for EC numbers on transport reactions might be beneficial to have further constraints...
It has been found that in the `manualModifications` function not all of the introduced changes to `Kcat` values are saved and given as an output. It actually happens that the...
`getEnzymeCodes` preferably queries SwissProt for EC code annotation and only when no match is found, it will look for EC codes annotation in KEGG. However, it is possible that the...
without a directly reproducible example, I note that upper bounds for protein draw reactions are often very small. With both cplex and glpk I have noted that this causes numerical...
As pointed out in https://github.com/SysBioChalmers/GECKO/pull/28, `adjust_pool_bounds` currently fails if it's used with 2 or more essential proteins = 0 (the resulting model does not grow). Fixing this is key for...
#### Description: **Issue:** The original implementation of `topEnzymeUsage` function calculates `protPool` by only considering the `prot_pool_exchange` flux. However, this does not reflect the total enzymatic capacity used by the metabolic...
### Description of the bug: For my research I'm using the ecYeastGEM model to evaluate what happens to fluxes if I incorporate certain knockouts or gene insertions in S. cerevisiae....
https://github.com/SysBioChalmers/GECKO/blob/1710a9861a60249207d547585cc96581e0ece18b/tutorials/protocol.m#L106 I ran this successfully when building a full ecModel, but got the error below when building a light ecModel: > Error using readDLKcatOutput (line 56) > Not all reactions...
There are 2 manual tests defined, one for Human-GEM and another for Yeast-GEM. Both seem to require a manual setup, but I believe it to be possible to get them...
With the intense development work over the last months, there is not always consistency on what kind of terminology is used. It is helpful to be consistent, and it is...
Metadata
Owner
Metadata
Toolbox for including enzyme constraints on a genome-scale model.