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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-enabled biochemical networks simulation environment to 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 the simulation modelling of the epidermal growth factor receptor microtubule-associated protein kinase pathway utility, a standalone simulation tool dedicated to the modelling and analysis of the epidermal growth factor receptor microtubule-associated protein kinase pathway. This builds on experiences from biochemical networks simulation environment by 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 middleware Condor. We present our results based on a case study with a model of the mammalian ErbB signalling pathway, a pathway strongly linked to cancer. [ABSTRACT FROM AUTHOR]

SUMMARY Many research institutions and Universities own computational capacity that is not effectively utilized, thereby providing an opportunity for such institutions to use such capacity to offer Cloud services (to both internal and external users). However, the unreliability and unpredictability of these resources mean that their use in the context of a Service Level Agreement (SLA) is high risk, leading to a reduction in reputation as well as economic penalties in case of SLA violation. We propose a methodology that addresses the issues of unreliability and unpredictability such that Cloud software services could be hosted upon volunteered resources. To enable the harnessing of these resources we rely on autonomic fault management techniques that allow such systems to independently adapt the resources they use based upon their perception of individual resource reliability. Using our approach we were able to scale out the backend infrastructure of the Cloud service elastically (min 30thinspaces per worker), opportunistically and autonomically. We address two key questions in this article: can a campus volunteer infrastructure be used in Cloud provisioning? What measures are necessary in order to ensure reliability at the resource level? Copyright © 2011 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

How can we measure the impact of an open-source software package over time? When a system has no price, no purchase contracts and no buyers or sellers it can be difficult to judge its impact on the world. To explore this issue, we have instrumented the Condor distributed batch system in a variety of ways and observed its growth to over 50 000 CPUs at over 1000 sites over five years. Instrumentation methods include automatic updates by e-mail and user datagram protocol (UDP), annotated download records and a voluntary user survey. Each of these metrics has various strengths and weaknesses that we are able to compare and contrast. We also explore the ethical and legal issues surrounding automatic data collection. Surprisingly, we discover that objections to automatic data collection are higher among people that are not using the Condor software. We conclude with some practical advice for further research into the measurement of software systems. Copyright © 2006 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

In this paper, we examine the issues of workflow mapping and execution in opportunistic environments such as the Grid. As applications become ever more complex, the process of choosing the appropriate resources and successfully executing the application components becomes ever more difficult. This may include extension or reduction of the initial workflow mapping as necessary for the actual execution. In this paper, we focus on the interplay between a workflow-mapping component that plans the high-level resource assignments and the workflow executor that oversees the component execution. We concentrate particularly on issues of data management and we draw from the experiences with mapping and execution systems: Pegasus, DAGMan and Stork. Copyright © 2005 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Since 1984, the Condor project has enabled ordinary users to do extraordinary computing. Today, the project continues to explore the social and technical problems of cooperative computing on scales ranging from the desktop to the world-wide computational Grid. In this paper, we provide the history and philosophy of the Condor project and describe how it has interacted with other projects and evolved along with the field of distributed computing. We outline the core components of the Condor system and describe how the technology of computing must correspond to social structures. Throughout, we reflect on the lessons of experience and chart the course travelled by research ideas as they grow into production systems. Copyright © 2005 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]