Tune repairModelLeaks branch with master - #47
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Two reactions (HMR_1572 and HMGCOAtx) were deleted in a previous model update, but after further investigation, it was found that there is not sufficient evidence/reason for their removal. This script will effectively undo their deletion, restoring all of their previous information into the model.
Add miscellaneous model curations
This update is implemented by running the script miscModelCurationScript_20181012.m. - Reactions HMR_1572 and HMGCOAtx that were removed by miscModelCurationScript_20180921.m are seamless restored here with the original indexes - 5 non-standard fields (e.g. rxnKEGGID) are removed
- This script is outdated and thus moved to `deprecated`.
Push to master for pre-release v0.4.2
Tune with master
Script moved to ComplementaryScripts/modelCuration/
Also updated some comments, and changed default output file extension from .txt to .tsv
The file writing feature is now available in a separate function, "writeRxnChanges".
Function takes the rxnChange structure generated from the docRxnChanges function, and exports it to a text (tsv) file.
Add curations for adding inner membrane compartment
This update is implemented by running the script curateMitochMembraneComp.m. - 4 duplicated reactions related to the electron transport chain were removed and updated to rxnAssoc.mat - 2 unused reactions were constrained as ub=lb=0 - 15 electrogenic proton-transporting rxns were constrained to prevent proton from [m] to [c] - 1 rxn LPAMtm was reversed in reaction direction - 58 electrogenic rxns involving proton transport between [m] and [c] were modified by replacing H+[c] with H+[i] - All modifications were saved to curateMitochMembraneComp_rxnChanges.tsv for tracking the changes
Push to master for pre-release v0.5.0
JonathanRob
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Oct 16, 2018
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Removed problematic file miscModelCurationScript_new.m. This file was not being actively used/maintained anyway.
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