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segrelab / comets

Computation of Microbial Ecosystems in Time and Space
GNU General Public License v3.0
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signals and toxins #30

Closed jeremymchacon closed 4 years ago

jeremymchacon commented 4 years ago

Hey Ilja, here's the pull that introduces signals and toxins. Looks like there might be some conflict with the commits that were done after I last pulled the segre/comets master -- let's figure that out.

Best,

Jeremy

mquintin commented 4 years ago

Cancelling request. Conflicts should be resolved on the branch before pulling to Master

dukovski commented 4 years ago

OK I'll check what's going on.

On Wed, Feb 26, 2020 at 11:44 AM jeremymchacon notifications@github.com wrote:

Hey Ilja, here's the pull that introduces signals and toxins. Looks like there might be some conflict with the commits that were done after I last pulled the segre/comets master -- let's figure that out.

Best,

Jeremy

You can view, comment on, or merge this pull request online at:

https://github.com/segrelab/comets/pull/30 Commit Summary

  • added Signal class with bare bones
  • FBAModel objects now optionally hold a list of Signal objects. FBACell calls on these to modify bounds of reactions based upon signal metabolite and boundary relationship.
  • MET_REACTION_SIGNAL loads from model file
  • signaling works with generalized logistic (aka Richards func). signals loaded in models have effect during simulation during calls to applySignals in run() of FBAModel.
  • various minor bugfixes to signaling
  • signals now have two functions to choose from
  • signals can now cause death and users can choose whether or not this also consumes the signal
  • fixed bug where deltaMedia was not initialized upon infeasible model
  • fixed bug in switch statement causing same function to be used during signaling no matter what was set
  • fixed a bug where models with biomass below cParams.getCellSize() were removed, causing NaNs in the totalbiomass log

File Changes

Patch Links:

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dukovski commented 4 years ago

Yes, correct. First branch, then pull.

On Wed, Feb 26, 2020 at 11:58 AM mquintin notifications@github.com wrote:

Cancelling request. Conflicts should be resolved on the branch before pulling to Master

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/segrelab/comets/pull/30?email_source=notifications&email_token=AAWJ2EQCNVXJHS77WYZCPBLRE2NUNA5CNFSM4K4JS2TKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENBA7VY#issuecomment-591531991, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAWJ2EWUDCAEML3KTTLQEZDRE2NUNANCNFSM4K4JS2TA .

-- Ilija Dukovski, Ph.D. Research Scientist Bioinformatics Program Boston University 44 Cummington St. Boston, MA 02215