GECKO
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SysBioChalmers
Toolbox for including enzyme constraints on a genome-scale model.
### Main improvements in this PR: **I hereby confirm that I have:** - [x] Tested my code with [all requirements](https://github.com/SysBioChalmers/GECKO) for running GECKO - [x] Selected `devel` as a target...
tl;dr: GAM estimation in `scaleBioMass` is wrong, proposed new solution in last paragraph. When the biomass composition is changed, the GAM should be reestimated. This is done by `scaleBioMass`, but...
Continuing [this](https://github.com/SysBioChalmers/ecModels/commit/f63ace2778146e5c6071d9732e83f4428d19ec3e) discussion, we should provide a way of treating models that were loaded from the .xml file, as they do not have `model.enzymes` and all associated fields (`model.enzGenes`, `model.enzNames`,...
Areas where we should improve documentation, as raised by @edkerk in a previous issue: - [ ] Clarify what the input and output parameters refer to for each function. -...
@BenjaSanchez @IVANDOMENZAIN In the new utilities branch #82, we required the input `oxPhosIDs` in the function `generate_protModels.m` , which is not so user-friendly. The reason that we requires this input...
Could somebody please double check the reaction catalysed by enzyme P07702 (Lys2). Compared to uniprot and SGD, I believe that the reaction in ecYeastGEM is incorrect. Best regards
This line (213) on gecko.py >protein_pool = self.metabolites.get_by_id('prot_{}_c'.format(protein_id)) should be >protein_pool = self.metabolites.get_by_id('prot_{}[c]'.format(protein_id)) This is not a problem with cobra 0.15.1. Don't know about 0.16.
It is not that straight-forward to generate models, integrate proteomics data and perform simulations with gecko. I have recently run into the following hurdles: - Lack of documentation. The [appendix](http://msb.embopress.org/content/msb/13/8/935/DC1/embed/inline-supplementary-material-1.pdf?download=true)...
In `measureAbundance`, the location of the protemics data is hard-coded. This is inconvenient if one would for instance have proteomics data for many conditions and want to make models for...
When I try to reproduce the figures from the paper (3A & 4B) with the model provided in GECKO toolbox 1.0.0 (ecYeast7_v1.0_batch.mat) following the supplementary information, my result doesn't match....
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Toolbox for including enzyme constraints on a genome-scale model.