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Protocol designs for hERG

This repo contains code to reproduce the work in "A range of voltage-clamp protocol designs for rapid capture of hERG kinetics" by Chon Lok Lei, Dominic G. Whittaker, Monique J. Windley, Matthew D. Perry, Adam P. Hill, Gary R. Mirams.

All protocol designs are provided as time series CSV files in protocol-time-series.

To run the code, run pip install -r requirements.txt to install all the necessary dependencies. Python >3.6 is required.

Content

  • optimise-bruteforce: Code to design hhbrute3gstep and wangbrute3gstep.
  • optimise-localsensitivity: Code to design hh3step and wang3step.
  • optimise-sobol: Code to design hhsobol3step and wangsobol3step.
  • optimise-square-wave: Code to design maxdiff.
  • rank-spacefill-protocols: Code to rank spacefill26, spacefill10 and spacefill19.
  • newton: Code to perform first round fitting with staircase, sis, hh3step and wang3step.
  • lib: Utility modules.
  • mmt-model-files: Model files for hERG.