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feat: include find energy generating cycles in the tests #48

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sulheim opened this issue Nov 14, 2018 · 1 comment
Open
1 of 5 tasks

feat: include find energy generating cycles in the tests #48

sulheim opened this issue Nov 14, 2018 · 1 comment
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feat new feature or request

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@sulheim
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sulheim commented Nov 14, 2018

Description of the issue:

The source code for running loopless fba and find energy generating cycles from Elad Noor (https://gitlab.com/elad.noor/stFBA) is present in the branch fix/check_infeasible_loops.
It would be nice to have this implemented as one of the tests in memote. Before we implement this we should make sure this is not on the roadmap for the memote development.
If we use the source code from Elad Noor we should consider how we do this in the most clean / appropriate way without getting too many dependent python packages.

Expected feature/value/output:

Automatic test of energy generating cycles in the memote-report

Current feature/value/output:

Can be run with the script
ComplementaryScripts/find_internal_and_unrealistic_energy-generating_cycles_scoGEM.py
Currently no energy generating cycles in the model.

To do:

  • Check with memote
  • Decide on how to use the Elad Noor source code (maybe just write it from scratch)
  • make it compatible with gurobi
  • include it in the custom tests so it can get into the memote report

I hereby confirm that:

  • A similar issue does not already exist
@sulheim sulheim added the feat new feature or request label Nov 14, 2018
@sulheim
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sulheim commented Dec 10, 2018

A similar method is already incorporated in memote, so I'm not sure if we really need this.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005494

sulheim pushed a commit that referenced this issue Mar 25, 2019
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