Functional Curation

The FunctionalCuration project is an add-on to Chaste aiming to provide a framework for a coherent approach to model fitting, simulation, comparison and validation. It does this by separate model structure (described in CellML) from details of the experimental scenario to apply to a model. Experiments are described in a protocol language extending SED-ML. For more details see the FunctionalCuration wiki pages.

The inaugural paper on Functional Curation is “High throughput functional curation of cellular electrophysiology models”, published in Prog Biophys Mol Biol in 2011, and the linked wiki page gives details of how to reproduce the results from that paper, having installed the necessary Chaste components and dependencies as set out below.

For work on applying Functional Curation to the cell-based side of Chaste, see our paper in ICCS2013.

Installation

This project requires the Chaste source tree to be installed, and you to have write access to your local copy, in order to be usable. You will thus need to install Chaste’s dependencies and build the Chaste software yourself. The easiest way to do this is using an Ubuntu machine (or an Ubuntu virtual machine) as discussed on InstallGuides/UbuntuPackage. For manual installation of each dependency, on any version of Linux, see DeveloperInstallGuide. Note that you will require those Chaste dependencies marked as ‘cardiac only’, and that this project requires at least version 1.39 of the Boost libraries. In order to generate result figures automatically, you will also need to install Gnuplot.

Note that it is advisable to install the source tree on local disk, rather than an NFS mount: we have experienced occasional problems in the latter case, depending on Linux distribution and version. Compiling Chaste is also fairly disk intensive, so benefits from local storage.

Having installed (and ideally tested!) the Chaste source tree, unpack this project as <Chaste>/projects/FunctionalCuration. It is crucial to match the folder name and location, or the project will not work.

If you wish to work with the latest version of the Chaste and project code, you can obtain them from the Chaste repository using the following commands:


#!sh
git clone -b develop https://chaste.cs.ox.ac.uk/git/chaste.git Chaste
cd Chaste/projects
svn checkout --username anonymous https://chaste.cs.ox.ac.uk/svn/chaste/projects/FunctionalCuration

Use your email address as the password for the ‘anonymous’ account.

Usage

Source code for the project is contained in the src folder, and tests of its functionality in tests. Annotated CellML files suitable for use with the framework are in cellml. Some additional interesting locations are:

  • tests/protocols contains example protocols
  • src/proto/library contains protocol libraries with functions available to all protocols
  • src/proto/parsing/protocol.rnc is a schema for the protocol XML language

See the sub-page for our main paper for details of how to reproduce its results. There are also many tests covering the lower-level functionality available for use by protocols. Run all the default tests with:


scons cl=1 b=GccOpt projects/FunctionalCuration

If you have multiple cores available, you can build in parallel with (using 4 cores for example):


scons -j4 cl=1 b=GccOpt projects/FunctionalCuration

To build an executable that can run a single protocol on a single model, do:


scons cl=1 exe=1 b=GccOpt projects/FunctionalCuration/apps

The executable will appear at projects/FunctionalCuration/apps/src/FunctionalCuration. You’ll need the environment variable LD_LIBRARY_PATH set up as described in the Chaste documentation in order to run it, since it needs to find the Chaste libraries and their dependencies.

For further information on using Chaste generally, see our extensive guide material. You may also wish to look at some of the basic user tutorials.

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