KDA Examples v0.3.0

What's Changed

• Updated both EmrE notebooks to store the net cycle fluxes for all cycles for the specific cases we look at in the kda paper. Notebooks now use EmrE cycles dictionary from other EmrE analysis code (transition flux analysis) for reproducibility (see #20)

• Fixed the table generated by the EmrE net cycle flux notebook for RAA biasing. Newly generated table has the flux values
  in the correct locations (see #21)

• Added KAPattern vs KDA comparison script along with the raw terminal output from the comparison (see #22)

• Added KDA runtime to KAPattern comparison as well as a script to measure KDA expression evaluation times (see #23)

Full Comparison: v0.2.0...v0.3.0

KDA Examples v0.2.0

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

KDA Examples v0.1.0

Initial release.