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Update BridgeDb swagger file to contain descriptionIdentifiers (Genes, proteins, metabolites, interactions)
Phase-out "metabolites" section
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When the order of models input to COBRA and then to COMETS changes, the results are changed.
cobra.io.read_sbml_model(model_1)
cobra.io.read_sbml_model(model_2)
has different results from:
cobra…
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#### Current behavior:
I was starting to work on implementing the changes I proposed in #609, and I noticed inconsistencies in the metabolite IDs for FMN and FMNH2 metabolites in different compartmen…
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#### Problem description
> Some biomass precursors are taken from the media and directly consumed by the biomass reaction. It might not be a problem for some ions or metabolites with known auxotrop…
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I noticed that OpenMS misses to correctly group some isotpe and adduct peaks.
This is based on FeatureFindingMetabo and MetaboliteFeatureDeconvolution.
In my opinion, the computation of the overla…
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I am attempting to use your hmdbQuery R package to pull metadata for a list of metabolites from hmdb. I am able to do this for about 215/366 metabolites. At this point, I am most interested in taxonom…
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Hi @oboforty,
The package sounds very nice and I would love to use it for a project. I followed the instructions for the installation, which seems to have worked fine (using PostgreSQL 12.11). Howe…
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### Description of the issue:
Based on the Memote report we find that the model has 645 universally blocked reactions, 137 orphan metabolites (only consumed, not produced) and 219 dead-end metabolite…
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@opencobra/cobrapy-core, @gregmedlock we need to make a design choice on the proposed groups and compartments PRs and I'd love to have everyone's input. My apologies that the issues were not very well…
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## Short description of the problem
"ValueError: max() arg is an empty sequence" was encountered after running anvi-reaction-network.
## anvi'o version
Anvi'o ..................................…