Fixing inconsitent metabolic tasks

[migp11]

Main improvements in this PR:

Metabolic_task_curation.xlsx
Inconsistent tasks were manually curated by correcting metabolite identifiers. To curate infeasible tasks, we manually adjusted upper and lower bounds for the input and/or output metabolites or by updating the compartments of some metabolites. After the curation process, 19 metabolic tasks were reconciled to the Human-GEM model, whereas 8 tasks remained either inconsistent (1) or infeasible (7). A summary of the curation processes can be found in the attached table. Curated tasks were tested by computing a feasible flux distribution using pFBA (scripts used can be shared if needed).

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[mihai-sysbio]

It appears the diff is getting complicated to review here. To avoid messing up the branches, I'd recommend cherry-picking the relevant commits onto a branch that stems from develop.

[migp11]

Hi,

Well, I took the time to add one single commit for each fixed task, therefore, the change in the diff corresponds to either modifying the bounds for inputs/outputs or updating the compartment of some of the metabolties. I can share the code I used to evaluate each task, but I've written it in Python using COBRApy and custom code, so it might be a better idea to use MATLAB code from this repo... my code just modify the mode to add the task, i.e. I create sources and sink reaction for input and output metabolites, respectibely and then just run a pFBA and check for feasibility; if the problem becomes feasible after adjusting the task bounds i check the flux distribution to see if the results obtained is biologically meaningful. That was more or less the adopted approach. Hope this helps!

My two cents!
Best
Miguel