Push to master for pre-release v0.6.1 - #70
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The function evaluates whether a model is properly balanced, such that mass and energy cannot be created from nothing, or in unrealistic amounts. This is not meant to be an exhaustive evaluation of a model's balance status, but a quick check of some key features.
tune with master
feat: get compartment maps
The Excel document can be used by RAVEN's checkTasks or parseTaskList functions to evaluate each of the metabolic tasks defined in the document for a given model. metabolicTasks_LeakCheck.xls contains 17 metabolic tasks that test for things such as generation of carbon and oxygen from nothing, phosphorylation of ADP (to ATP) with no inputs, and realistic ATP generation per glucose consumed. This task list can therefore replace the existing "checkEnergyMassLeaks" function, as it is a more exhaustive and straightforward evaluation.
ID numbers are added to each task so that they can be more easily referenced.
Each model change made in repairModelLeaks now references a specific metabolic task ID number(s) (corresponding to ID numbers in the metabolicTasks_LeakCheck.xls task file) which the change is supposed to address.
No longer used.
- Gather together deleted/constrained reactions in this centralized file for easy manipulation in the future
- Since the reaction constraining and bound/coefficient adjustment form an integrated work, only the overall implementation can achieve all the metabolic tasks listed in `metabolicTasks_LeakCheck.xls`.
- The script documentation is modified by adding the information about reaction constraining, which is an indispensable part for coherent repairing of mass/energy leaks in the model.
fix: continuous repairing model leaks
This update is implemented by running script `repairModelLeaks.m`: - this curation work is explained in #33 - 41 reactions are modified by adjusting reaction bounds and/or stoichiometry - 236 reactions (including 12 that were also modified in bounds/stoichiometry adjustment) are constrained in order to achieve the metabolic tasks listed in `metabolicTasks_LeakCheck.xls`. These inactivate reactions are archived in `inactivationRxns.tsv` - All modifications are saved to `repairModelLeaks_rxnChanges.tsv` for tracking the changes
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