Chris Bradley, postdoctoral scientist at Oxford University's Department of Physiology, Anatomy and Genetics, will give a talk on Friday 1 February in Oslo entitled: OpenCMISS for coupled electro-mechanical modelling of the heart.
Time: Friday 1 February, 10.00 - 11.00
Place: "Lille auditorium", Dept of Informatics (Ifi), University of Oslo, Gaustadalleen 23.
Increased computational power over the last few decades has allowed for increasingly complex and anatomically accurate models of biological systems which incorporate multiple physical processes. An example of such a model is the Auckland Heart model which incorporates a number of important factors in the generation of a heart beat including electrical activation of the myocardium, ventricular mechanics and fluid mechanics of the coronary blood vessels. The Auckland heart model uses a custom computer package called CMISS to numerically solve the equations resulting from the model. CMISS is comprised of two parts: cmgui - a graphical front end written in C/C++ and cm - the computational engine written over the last 25 years in Fortran 77 and parallelised using OpenMP for shared memory multiprocessing. The desire to solve larger and more complicated models using CMISS has been hampered by scalability limits inherent in shared memory computing. To overcome these limits it has been decided to re-engineer the computational engine in CMISS using MPI to allow it to run on distributed memory parallel computers. The new computational code, named openCMISS, is written in Fortran 95 and is open source. The new code will use emerging XML definition languages (CellML for cellular models and FieldML for spatially varying components) in order to provide flexibility for the modeller. This talk will introduce the ideas behind modelling electrical activation and ventricular mechanics in the heart. It will then discuss the framework of openCMISS with a view to illustrating how these heart modelling problems will be solved.
All computer scientists, mathematically and computationally inclined biologists, and all others interested in the modelling of biological systems incorporating multiple physical processes are welcome to come to the talk, which is hosted by CIGENE and USIT, the University of Oslo's Centre for Information Technology
