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Fighting cancer and modeling human hearts: Chaste 2.1 released

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Researchers from the Computational Biology Group at OUCL are developing simulation software for modeling biological systems such as the workings of the heart or the growth of tumours. This software will ultimately improve the understanding of cardiac drugs and the treatment and care of patients with cancer. The latest version of the Chaste software has being released under an Open Source software licence meaning researchers from across the globe are now benefiting from it.  Chaste contains generic libraries of computer code which are aimed at general computational biology problems together with programs that tackle two big killers: cardiac disease and cancer.

Although computerized models aren’t new, the Chaste (Cancer, Heart and Soft Tissue Environment) project aims to develop a significantly more sophisticated, and much faster simulation model those currently used. It draws on expertise from software engineering, high performance computing, mathematical modeling and scientific computing, to enable cardiac physiologists, pharmaceutical companies and clinicians to understand the human heart better: from a whole organ level, right down to the tissue, and cell level.

The cardiac software has been tested in conjunction with Fujitsu's European Laboratory, to ensure that it can be used with confidence by the heart modeling community. 

Improvements to the 2.1 release include:

  • The user documentation has been significantly extended and tutorials written for the cardiac executable.
  • The standalone binary now has a folder of dependency libraries and a wrapper script Chaste.sh which ensures that these libraries are linked when the program is run.
  • The integration of CellML models of cardiac cells has been significantly improved. Code for all cell models shipped with Chaste is now generated on-the-fly from CellML.
  • Various simulation parameters can now be changed via the XML file when resuming from a checkpoint.
  • Chaste is now able to read meshes from Triangle, Tetgen, Meshalyzer or VTK format based solely on the basename of the files.
  • Cell-based Chaste includes source code for simulating vertex-based discrete cell population models.

The new release of Chaste 2.1 is available to download as open source or as standalone cardiac executable from http://web.comlab.ox.ac.uk/chaste/download.html

 

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