sokrypton / sokrypton/ColabFold

Edit Internal Configurations of AlphaFold Pipeline when using ColabFold notebooks

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Jupyter Notebook
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Description

Hi again!
I had a question regarding changing some internal configurations in the code. If I understood correctly, when we use the ColabFold notebooks we connect to its servers to do MSA construction and retrieve its results, and then the rest of evoformer and structure module pipeline is done by the colab environment, right? considering this it seems possible to change some portions of the code and internal configurations, and still be able to use the changed code with notebooks on the google colab environment. I was wondering if this is possible and how can this be done?
For example, suppose I want to change the default parameter value of one of the main functions of alphafold prediction pipeline, how can I change that and run the altered code with ColabFold notebooks?
Best,

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the ColabFold notebooks and the AlphaFold prediction pipeline entry points to determine which internal parameters run in Colab and which work is delegated to remote services. Document whether changing a main-function default is supported, how altered code can be loaded in the notebook, and the limits of that workflow.

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Assessment

Tech stack
jupyter-notebook
Domain
bioinformatics
Issue type
Documentation
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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