sokrypton / sokrypton/ColabFold
API for ColabFoldDB/mmseqs2 versions
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Description
Hi ColabFold!
we are using this function to run mmseqs2 remotely using this remote API: https://api.colabfold.com/
I am trying to keep track of the databases and sequence searching tools versions used for modeling in the special metadata.json file. Would it be possible to extract the mmseqs2 version and versions of the used databases (e.g. ColabFoldDB) from its API? If not, how often do you update the dbs/mmseqs and is it possible to obtain these versions programmatically?
Many thanks!
Dima
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reading colabfold/batch.py around line 719 and tracing how the remote API at api.colabfold.com is called. Determine whether the API currently exposes mmseqs2 and database versions, then define the metadata or endpoint behavior needed to identify the versions and update cadence programmatically.
Written by the indexing model from the issue text.
Assessment
- Domain
- api, bioinformatics, databases
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100