v2024.1

A release of ApPredict for compatibility with Chaste v2024.1.

What's Changed

• See Chaste's release notes for knock on effects (e.g. we now have to build with cmake and no longer scons).
• Using cmake as the build system has enabled us to download, convert and compile only the subset of the CellML files from www.github.com/Chaste/cellml that ApPredict really needs, instead of having all of them in git submodule. This massively speeds up compilation times.

Full Changelog: v2021.1...v2024.1

ApPredict for use with Chaste 2021.1

This version of ApPredict is compatible with Chaste 2021.1 which can be downloaded here.

What's Changed

• Switching to Model factory method by @MauriceHendrix in #10
  • Users now supply the model which should be used with --model this can be:
    • a path to a CellML file (relative or absolute) for runtime CellML conversion, OR
    • a CellML model name (filename without the .cellml) for using any CellML included at compile-time, OR
    • an old hardcoded integer choice (deprecated).
• forced hund_rudy_2004 not to use the analytic jacobian. by @MauriceHendrix in #5
• Switching off analytic jacobian (generated by codegen) by default by @MauriceHendrix in #7

Setting up automated github testing

• Adding ApPredict GitHub Actions workflow on self-hosted Ubuntu 20.04 runners by @kwabenantim in #11
• #3099 Add failed test notifications for Slack by @kwabenantim in #12
• #3099 Fix force-failed test suite by @kwabenantim in #13

Full Changelog: v2019.1...v2021.1

ApPredict for use with Chaste 2019.1

This version of ApPredict is compatible with Chaste 2019.1 which can be downloaded here.

Release Notes

As with Chaste, ApPredict is now compiled with C++14, so dependencies are a bit newer.

Speed

Solution of the O'Hara-Rudy 2011 and O'Hara-Rudy-CiPA 2017 models has been speeded up considerably (40-50%) by using a two-step solve process which resets the solver before and after the pacing stimulus is applied. Minor improvements for other models too. Although I've also made solver tolerances a bit finer, which helps steady-state detection, but means not much change to speed overall.

Otherwise minor changes to lookup table manifest file handling for uncertainty quantification. A fresh copy of lookup tables available on the server is downloaded whenever we have web access.

ApPredict for use with Chaste 2018.1

ApPredict 2018.1

This version of ApPredict is compatible with Chaste 2018.1 which can be downloaded here.

Release Notes

CiPA-related Features

• The FDA's version of the CiPA O'Hara-Rudy Dynamic Model (CipaORdv1) can now be used with the argument --model 8, and we have also made it available for anyone else to use via the CellML repository.

• The FDA's qNet metric can now be calculated and output. This happens automatically when --model 8 --pacing-freq 0.5 is used.

Specifying test concentrations by file (for PKPD runs)

• If you want to run at concentrations in a file instead of specifying at command line, you can do --pkpd-file <relative or absolute filepath>.
• To evaluate APD90s throughout a set of up to N profiles of free concentration through time please provide a file with this data format for each row:
  Time(any units)<tab>Conc_trace_1(uM)<tab>Conc_trace_2(uM)<tab>...Conc_trace_N(uM)

Lookup tables

• Improvements have been made to the Lookup Tables (used for uncertainty quantification) and now the lowest dimensional lookup table that is available for the ion channels of interest will be downloaded and used automatically. If you are using this feature please let me know as it may change a bit in future...

ApPredict for use with Chaste 2017.1

ApPredict 2017.1

Release Notes

• October 2017 - there are now some new error codes to get more fine-grained information out when APD evaluations fail, or there is unusual behaviour that might want to be classed separately (see https://chaste.cs.ox.ac.uk/trac/wiki/ApPredict).
• April 2017 - ​fa8a3a4 The LookupTableGenerator (for uncertainty quantification calculations) is now a bit better at detecting 'No depolarization' because it does a pre-run with sodium channel blocked and sets the threshold for an action potential to be higher than the voltage achieved here.
• Nov 2016: ​2361a19 downsampling was improved to provide nicer visual plots.

ApPredict for use with Chaste 3.4

A release of ApPredict to work with Chaste 3.4