2024-04-16
PAMREIN's daily Open Notebook (COMMONS Lab)
Todo - Check Github
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Meetings
Daily report (What did I learn?)
Today I got the advice to look for the rules (general and intermediat). The goal is to change the rules, depending on the organism.
So for the moment I didn't dig more into the feasibility filter. I stopped by the "_choose_items_to_filter" function, which was correct, but somehow the filtering still doesn't work. I should look into it a little bit more maybe later.
For the reaction rules I found following information: ./MINE-Database/mine_database/data/metacyc_rules/ metacyc_intermediate_rules.tsv - 7359 lines () metacyc_generalized_rules.tsv - 1225 lines (JN1224min from https://doi.org/10.1016/j.ymben.2021.02.006)
the loaded rules in pickaxe is the generalized_rules (./MINE-Database/mine_database/rules.py).