Computational Tools & Techniques

The core research interests of the Computational Bioengineering Laboratory often require relatively complex computational tools and techniques. The multi-scale problems are also very computationally demanding. For this reason, we have been interested in proposing efficient numerical techniques and developing efficient software.

Numerical techniques for differential equations

The mathematical descriptions of physiological systems typically involve ordinary and partial differential equations (ODE and PDE respectively). Often the simultaneous solution of ODE and PDE is required. We have extensive experience in various techniques such as the Finite Element Method (FEM), Finite Difference Method (FDM) and Boundary Element Method (BEM).

Reference Publication:

Buist ML, Sands G, Hunter P and Pullan A. A deformable finite element derived finite difference method for cardiac activation problems. Ann Biomed Eng, 31(5):577–588, May 2003. (doi:10.1114/1.1567283)

Software development and use

Over the years, the staff at the Computational Bioengineering Laboratory gained direct experience in developing tools to be applied in computational biology. Members of the lab have been active developers of very popular multi-physics packages such as CMISS or very powerful parallel FEM open-source solvers such as Chaste. We have expertise in a variety of computer languages including C/C++, Fortran, Perl, Python, Matlab and Scilab.

Chaste Logo CMISS Logo