Speeding up systems biology simulations of biochemical pathways using condor
Xuan Liu, Simon J. E. Taylor, Navonil Mustafee, Jun Wang, Qian Gao, David Gilbert · Concurrency and Computation Practice and Experience · 2013
SUMMARY Systems biology is a scientific field that uses computational modelling to study biological and biochemical systems. The simulation and analysis of models of these systems typically explore behaviour over a wide range of parameter values; as such, they are usually characterised by the need for nontrivial amounts of computing power. Grid computing provides access to such computational resources. In previous research, we created the grid‐enabledbiochemical networks simulation environmentto attempt to speed up system biology simulations over a grid (the UK National Grid Service and ScotGrid). Following on from this work, we have created thesimulation modelling of the epidermal growth factor receptor microtubule‐associated proteinkinase pathway utility, a standalone simulation tool dedicated to the modelling and analysis of theepidermal growth factor receptor microtubule‐associated protein kinase pathway. This builds on experiences frombiochemical networks simulation environmentby decoupling the simulation modelling elements from the Grid middleware. This new utility enables us to interface with different grid technologies. This paper therefore describes the new SIMAP utility and an empirical investigation of its performance when deployed over a desktop grid based on the high throughput computing middlewareCondor. We present our results based on a case study with a model of themammalian ErbB signalling pathway, a pathway strongly linked to cancer. Copyright © 2013 John Wiley & Sons, Ltd.