RosettaCommons / RosettaCommons/atomworks
Extend `AtomWorks` for sequence-based tasks
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- Dominant language
- Python
- Stars
- 446
- Forks
- 52
- PR merge metrics
- No merged PRs in 30d
Description
In theory, the AtomWorks library could be trivially extended to support sequence use cases as well.
Instead of the AtomArray, Biotite's sequence could be used as the common representation maintained throughout a Transform pipe. We'd need a different way of loading files as well since parse or load_any are no longer appropriate.
The main benefit of incorporating sequence-based functionality would be (1) access to pre-built datasets/parsers (2) training infrastructure (3) integration of sequence and structure
Contributor guide
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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
The issue names no files or tests. Start by reviewing the Transform pipeline and how parse or load_any currently load AtomArray inputs, then compare that flow with biotite.sequence. Done means the scope for sequence loading, shared representations, dataset and parser access, training infrastructure, and sequence–structure integration is defined.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100