Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

get enzyme sequences from all available sources #37

Open
ckouder opened this issue Jun 26, 2024 · 0 comments
Open

get enzyme sequences from all available sources #37

ckouder opened this issue Jun 26, 2024 · 0 comments
Assignees

Comments

@ckouder
Copy link
Collaborator

ckouder commented Jun 26, 2024

Mohit provides a notebook that helps us to gather enzyme sequences from different databases. We should use this notebook in novostoic backend to allow users to select enzyme sequences with maximum visibility.

Approach

  1. Test the notebook with different reaction ids from https://github.com/mohovision/novoStoic2.0/blob/dev/notebooks/all_refs_in_all_rules.json
  2. Add sleep commands to prevent Kegg API from freezing
  3. (Maybe) Run notebooks on all reaction ids and save the results somewhere related save pre-calculated enzyme sequences of each reaction-id #36
    (ASSUMPTION: the enzyme sequences of each reaction will mostly remain the same - maybe they will add new enzyme sequences for each reaction)
    (ASSUMPTION: all_refs_in_all_rules.json do not change quite often)
  4. Get enzyme sequences for each rule, gather the compound, and calculate the activity scores
    In this step, we need to compose the input for enzyme rank - that is <primary identifier>:<enzyme sequence>
@ckouder ckouder self-assigned this Jun 27, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant