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Fix/biomass composition #159

Merged
merged 7 commits into from
Sep 10, 2018
Merged

Fix/biomass composition #159

merged 7 commits into from
Sep 10, 2018

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BenjaSanchez
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Main improvements in this PR:

  • redefined biomass composition to fix previous bug that underestimated the biomass content (previously water was included in polymers, i.e. was adding to less than 1 g/gDW).
  • added folder ComplementaryData/physiology for biological data of yeast (biomass composition, chemostat data and the like)
  • fitted GAM to chemostat data

Current composition for the model, according to sumBioMass.m, is now:

protein      -> 0.46 g/gDW
carbohydrate -> 0.3857 g/gDW
RNA          -> 0.061 g/gDW
DNA          -> 0.0037021 g/gDW
lipid        -> 0.087299 g/gDW
other        -> 0.0022946 g/gDW
total        -> 1 gDW/gDW
Growth = 0.087907 1/h
GAM    = 55.4 mmol/gDWh

I hereby confirm that I have:

  • Tested my code with all requirements for running the model
  • Selected devel as a target branch (top left drop-down menu)
  • If needed, asked first in the Gitter chat room about this PR

biomass composition was first switched back to the original model (Forster et al. 2003) except for lipid data that was kept as the current one. Coefficients for s_0001 & s_0004 were also fixed based on modelCorrections.m
rescaled some values with data from a recent study with reasonable lipid content (Lahtvee et al. 2017)
to have biomass add up to 1
GAM is now fitted to simulate chemostat data of S. cerevisiae at low growth rates (Van Hoek et al. 1988)
@BenjaSanchez BenjaSanchez added the bug something is wrong in the model label Sep 7, 2018
@BenjaSanchez BenjaSanchez self-assigned this Sep 7, 2018
@BenjaSanchez BenjaSanchez requested a review from feiranl September 7, 2018 15:10
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@feiranl feiranl left a comment

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Great!

@feiranl
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feiranl commented Sep 8, 2018

May I start a new branch to add more biomass components or just add them in this branch?

@BenjaSanchez
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@feiranl as this is a fixing branch and you intend to introduce new things (i.e. a feature branch), the proper thing to do is to work on a separate branch. Will merge this one tomorrow.

@BenjaSanchez BenjaSanchez merged commit 3a8931e into devel Sep 10, 2018
@BenjaSanchez BenjaSanchez deleted the fix/biomassComposition branch September 18, 2018 15:04
@BenjaSanchez BenjaSanchez mentioned this pull request Sep 26, 2018
@feiranl feiranl mentioned this pull request Nov 1, 2018
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@edkerk edkerk mentioned this pull request Sep 15, 2022
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2 participants