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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.
Test the notebook with different reaction ids from https://github.com/mohovision/novoStoic2.0/blob/dev/notebooks/all_refs_in_all_rules.json
Add sleep commands to prevent Kegg API from freezing
(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)
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>
The text was updated successfully, but these errors were encountered:
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
https://github.com/mohovision/novoStoic2.0/blob/dev/notebooks/all_refs_in_all_rules.json
(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)In this step, we need to compose the input for enzyme rank - that is
<primary identifier>:<enzyme sequence>
The text was updated successfully, but these errors were encountered: