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fix: biomass tests from memote #138

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BenjaSanchez opened this issue Jul 13, 2018 · 1 comment
Open
5 of 8 tasks

fix: biomass tests from memote #138

BenjaSanchez opened this issue Jul 13, 2018 · 1 comment
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memote anything related to the memote report standby work somewhere else is needed before advancing

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@BenjaSanchez
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BenjaSanchez commented Jul 13, 2018

Description of the issue:

From the latest memote report, the following biomass tests are giving unexpected results:

  • Biomass consistency = 0
  • GAM is not detected (the test errors) is detected
  • Unrealistic Growth Rate In Default Condition = true false
  • Ratio of Direct Metabolites in Biomass Reaction = 0.7 0.14
  • Number of Missing Essential Biomass Precursors = 37 30

Many of these tests failing may be a result of an improper detection of our biomass pseudoreaction as "clustered", i.e. separated into protein pseudoreaction, lipid pseudoreaction, etc.

More relevant info at opencobra/memote#243

I hereby confirm that I have:

  • Tested my code with all requirements for running the model
  • Checked that a similar issue does not exist already
  • If needed, asked first in the Gitter chat room about the issue
@BenjaSanchez BenjaSanchez added help wanted feel free to help us solving this issue! memote anything related to the memote report labels Jul 13, 2018
@ChristianLieven
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Unrealistic Growth Rate In Default Condition = true is likely a bug in memote, I've seen it a couple of times now in models which should be fine. I'll have to dig around more to pinpoint the cause though!

@BenjaSanchez BenjaSanchez added standby work somewhere else is needed before advancing and removed help wanted feel free to help us solving this issue! labels Nov 1, 2018
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Labels
memote anything related to the memote report standby work somewhere else is needed before advancing
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