David Steinberg

Bioschemas FAIR Checker for Croissant metadata via Leyla https://fair-checker.france-bioinformatique.fr/

We are discussing using this tool for creating a "dataset of datasets" as part of the MLCommons Datasets WG. Received this comment regarding that in the latest Datasets WG call...

Welcome @lubianat we would love to have your input and drive future development! There's a number of topics in this issue that could be taken up. You might be interested...

Hi @bwalsh !! I put in a cursory benchmark in the above issue. The code here uses your CPU count, which for me was 12. It took a little less...

This should make it so we can have the "small seqrepo" versions of vrs-python easily installed via bioconda https://tertiary-workflows-docs.readthedocs.io/en/latest/writing_bioconda_recipes.html

Thanks @mbaudis, This is great! It shows how the ga4gh data model can be used to model a wider variety of genomic features in a standard way. In the first...

Yes, that question, and also how do we handle the fact that alternate bases can be multiply valued if we are only providing the single sv annotation. I also prefer...

The variant data model has the alternate bases as an array. I believe you're suggesting that for variants with `svlen` info tags, this alternate bases entry will be empty. It...

Excellent discussion! For this issue, let's close when variant type, svlen, and cipos/end have been added to the variants schema. Please leave your input on whether the proposed representation at...

If we go with this approach then we have to enforce that reference IDs are used when constructing position requests. The reason being, we no longer have uniqueness guarantees of...