cjmyers

We are doing sequence search using Vsearch (https://vcru.wisc.edu/simonlab/bioinformatics/programs/vsearch/vsearch_manual.pdf). We have also struggled to figure out how to configure it to give "close" but not "exact" results. If you have any...

https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/so-simple.json

I disagree with this one. The page for parts is already so full. Adding the sequence will overload this page even further. I think the sequence should only be visible...

The ideal in my mind would be to make this part of the Visbol diagram, namely, you could swap tabs between visual and sequence view like on the iGEM website....

Also include /summary and add to api docs too (returns JSON)

/metadata and /summary return JSON, must compare with diff /download returns an attachment, so if you attach a text, can compare with diff All other use SBOL Validator

Good catch. This is clearly an error in the iGEM dataset. Indeed, when we converted the iGEM data set to SBOL, we found 834 parts with errors like this one....

Thanks for your detailed description. We have been able to reproduce this issue with our VisBol2 tool, and we will try to find a solution soon. In the future, you...

The issue related to the resolveBatch size in the config.json, which was set to 50. This created a SPARQL query that was too large. Reducing the resolveBatch size to 20...

GenBank is not a valid download type for Sequences. If you use this link, it works: https://synbiohub.org/public/igem/BBa_E0040/1/gb Granted, you should get an error message and not an empty file.