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There has been some back and forth on this. Currently (Oct 2019) we convert regulation by small molecules in Reactome to regulation by binding reaction in go-cams. Like this in Glycolysis.
![Sc…
goodb updated
4 years ago
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Apologies if this is actually a trivial error on my part - it's my first time playing around with COBRA / metabolic models.
I am using ModelSEED to generate a SBML model of _Vibrio natriegens_ and …
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## User feedback
Feedback from ClimApp testers (1st beta version). All feedback will be listed here, the rate with which we implement the changes (and whether we are going to implement the changes) w…
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succinate-semialdehyde dehydrogenase
I wondered if this were a littl indirect for
ALDH5A1 | Succinate-semialdehyde dehydrogenase, mitochondrial | | glutamate metabolic process | | UniProt …
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I've been taking a look at the annotation sets that we currently import into the GOA database and that have been identified as being unmaintained, namely those from JCVI/TIGR and PAMGO_Mgrisea.
I'v…
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We probably want to evolve this repository into a 'grasp 2.0' kind of application - I think it would be nice to think of a new name for the application as the usage and output will be pretty different…
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### Description of the issue:
The current `humanGEM` model contains five different biomass reactions:
- `biomass_reaction`, `biomass_maintenance`, and `biomass_maintenance_noTrTr` from Recon3D
- `b…
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We have a reference PMID:30566857 which reports a model of 'healthful obesity' or metabolically healthy/normal obesity. There is not currently an appropriate DO term for this. These mice are modeling …
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load metabolic networks alongside the non-metabolic ones
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Consider the ode model:
```
r = te.loada('''
x' = k1/(1+y^n1) - k2*x;
y' = k3/(1+x^n2) - k4*y;
x = 4; y = -4;
k1 = 12; k3 = 12; k2 = 2; k4 = 2
n1 = 4; n2 = 4
''')
…