Grid-enabled SIMAP utility: Motivation, integration technology and performance results

Abstract

A biological system comprises large numbers of functionally diverse and frequently multifunctional sets of elements that interact selectively and nonlinearly to produce coherent behaviours. Such a system can be anything from an intracellular biological process (such as a biochemical reaction cycle, gene regulatory network or signal transduction pathway) to a cell, tissue, entire organism, or even an ecological web. Biochemical systems are responsible for processing environmental signals, inducing the appropriate cellular responses and sequence of internal events. However, such systems are not fully or even poorly understood. Systems biology is a scientific field that is concerned with the systematic study of biological and biochemical systems in terms of complex interactions rather than their individual molecular components. At the core of systems biology is computational modelling (also called mathematical modelling), which is the process of constructing and simulating an abstract model of a biological system for subsequent analysis. This methodology can be used to test hypotheses via insilico experiments, providing predictions that can be tested by in-vitro and in-vivo studies. For example, the ERbB1-4 receptor tyrosine kinases (RTKs) and the signalling pathways they activate, govern most core cellular processes such as cell division, motility and survival (Citri and Yarden, 2006) and are strongly linked to cancer when they malfunction due to mutations etc. An ODE (ordinary differential equation)-based mass action ErbB model has been constructed and analysed by Chen et al. (2009) in order to depict what roles of each protein plays and ascertain to how sets of proteins coordinate with each other to perform distinct physiological functions. The model comprises 499 species (molecules), 201 parameters and 828 reactions. These in silico experiments can often be computationally very expensive, e.g. when multiple biochemical factors are being considered or a variety of complex networks are being simulated simultaneously. Due to the size and complexity of the models and the requirement to perform comprehensive experiments it is often necessary to use high-performance computing (HPC) to keep the experimental time within tractable bounds. Based on this as part of an EC funded cancer research project, we have developed the SIMAP Utility that allows the SImulation modeling of the MAP kinase pathway (http://www.simap-project.org). In this paper we present experiences with Grid-enabling SIMAP using Condor.