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KDA Examples v0.2.0

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@nawtrey nawtrey released this 08 Mar 03:02
· 6 commits to master since this release
v0.2.0
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What's Changed

Full comparison: v0.1.0...v0.2.0

KDA Paper Code Consolidation

  • Created new directory kda_paper to store all paper-related code, with detailed
    README containing instructions for generating all paper figures and data
  • Moved EmrE code into kda_paper with updated README
  • Added all scripts from kda-paper repo to kda_paper

EmrE Updates

  • Combined net cycle flux and stoichiometric ratio figures into single figure with stacked subfigures
  • Added figure for all EmrE cycles
  • Changed Roff flux diagrams to generate only the diagrams for kAA = 100 and Roff = 1e-10, 1e0, 1e2
  • Fixed k86 variable substitution issue. k86 in EmrE paper is shown to have values of H_off when
    it should be D_off. This carried through to the variable subs in fig_7a.py, which now correctly
    assign H_off. Also corrected in fig_7b.py, and sympy functions were updated to reflect the change.
  • Updated to save all figures as .png, .svg, and .pdf
  • Added code to output .csv of plot data for all EmrE figures
  • Added notebooks for analyzing EmrE operational fluxes in terms of individual net
    cycle fluxes, normalization factor, etc. for the RAA and Roff cases

Misc Updates

  • Added notebook for KDA Demo/Antiporter Tutorial
  • Updated the 4-state model notebook to have correct variable substitutions
    for an antiporter model, consistent with the KDA paper
  • Added script to compare the operational fluxes for the 6-state antiporter model (now located in kda_paper)
  • Added script to compare the operational fluxes for the 8-state model of EmrE (now located in kda_paper)
  • Added error propagation analysis in notebook for 6-state antiporter model G1
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