fix metabolicTasks_CellfieConsensus

[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

[edkerk]

The messy PR is due to the commits having been made on a remote main branch, instead of a develop branch. I have resolved this locally by rebase-ing, this will be resolved when changes are pushed (only the data/metabolicTasks/metabolicTasks_CellfieConsensus.txt file is modified).

We do not use the CellfieConsensus tasks, so it would be very challenging to fully review these changes. However, they seem to make sense, and do not seem to break something that was working before. I therefore approve the PR.

[edkerk]

Resolving the conflicts ended up in commiting the changes here: 30b3da8. This PR will therefore be closed, the changes are applied in develop.