Characterization of the kinetic and conformational properties of channel proteins is a crucial element in the integrative study of congenital cardiac diseases. The proteins of the ion channels of cardiomyocytes represent an important family of biological components determining the physiology of the heart. Some computational studies aiming to understand the mechanisms of the ion channels of cardiomyocytes have concentrated on Markovian stochastic approaches. Mathematically, these approaches employ Chapman-Kolmogorov equations coupled with partial differential equations. As the scale and complexity of such subcellular and cellular models increases, the balance between efficiency and accuracy of algorithms becomes critical. We have developed a novel two-stage splitting algorithm to address efficiency and accuracy issues arising in such modeling and simulation scenarios. Numerical experiments were performed based on the incorporation of our newly developed conformational kinetic model for the rapid delayed rectifier potassium channel into the dynamic models of human ventricular myocytes. Our results show that the new algorithm significantly outperforms commonly adopted adaptive Runge-Kutta methods. Furthermore, our parallel simulations with coupled algorithms for multicellular cardiac tissue demonstrate a high linearity in the speedup of large-scale cardiac simulations.

SUMMARY: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided. AVAILABILITY: The HNB portal is available at http://www.hnbioinfo.de