fix: continuous repairing model leaks - #69
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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.
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.
JonathanRob
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Nov 23, 2018
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This looks good, and is a big improvement over the original implementation, in my opinion.
edkerk
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Jul 14, 2026
Install raven-toolbox from fix/ftinit-raven-parity (PR #69) so the gene essentiality workflow picks up the corrected task-essential-reaction discovery, which now matches RAVEN's checkTasks (397 essential reactions on Human-GEM v2.0.0 instead of 259). Revert to the default branch after that PR merges.
edkerk
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Jul 15, 2026
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Main improvements in this PR:
metabolicTasks_LeakCheck.xlsfor evaluating the performance of fixing mass/energy leaks in the model, and add ID number to each taskrepairModelLeaks.mby referencing specific metabolic task ID number(s) to the corresponding section that supposed to address the issue. Note that only overall implementation of the changes in this script can achieve those targeted metabolic tasksI hereby confirm that I have:
develas a target branch