sokrypton / sokrypton/ColabFold
AlphaFold Colab: Long residues >3000 in colab pro +
Open
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
Purchased colab pro + to run larger sequences but the session keeps failing because it is running out of memory. I switched the running time to premium and high ram as suggested when I upgraded to colab pro +
Is there any way that AlphaFold can predict larger sequences?
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
No file, test, or entry point is identified in the issue. Start by reproducing the memory failure for sequences longer than 3000 residues in the Colab Pro+ high-RAM and premium settings, then inspect the notebook workflow and existing issue context; done would require a documented way to complete such predictions or a clearly scoped limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, cloud, machine-learning
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100