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A toy model of metabolism consisting of 3-4 reactions (glucose import & subsequent conversion) will be integrated with the submodules changing protein counts np of the enzymes catalyzing the metabolic…
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This could look like this: Make list of fields that can contribute to type ahead (e.g. IDs, protein and disease names, etc,.) Performance is crucial.
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The current version requires:
>
> For each complex you want to predict, you need a directory containing the ligand and protein file. For example:
>
> ```
> DSDP_dataset
> └───name1
> │ …
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Dear all,
Thanks for the development of this nice tool. We ran it on our dataset of serum samples analyzed with SomaLogic v4.1 data in 130 patients.
We did get results but also many of the org…
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**Is your feature request related to a problem? Please describe.**
The issue is picking a predicate for drugbank descriptions of genes/proteins that are linked to chemicals (keywords like enzyme, car…
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This line should be querying CDS, not transcript
https://github.com/openvax/pyensembl/blob/1231e965e5a5c849e3242030742b6f6200b2de68/pyensembl/genome.py#L580
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Between 8am and 4pm PT, on July 4th, the ontology build started to fail, bringing down or blocking multiple pipelines. Looking at the PRs in that window, I suspect the changes happened earlier, but to…
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First copy [this file](https://github.com/PNNL-CompBio/p3/blob/main/functional/calculate-functional-enrichment.Rmd) to this repo. Then we can run the three tests on the protein data (syn25706561) and …
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Hello,
For GO annotations and network representation (we're using esyN - www.esyn.org), we would find it very useful to have a set of PRO entries for S. pombe complexes. We maintain a list of GO ce…
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Hi Matt,
A girl in my lab is trying to set up ITEP with some bacterial genomes. She ran into an issue: convertGenbank2table.py fails because some of here genbank files (downloaded from RAST) have join…