Some challenges facing scientific software developers: The case of molecular biology

It is apparent that the challenges facing scientific software developers are quite different from those facing their commercial counterparts. Among these differences are the challenges posed by the complex and uncertain nature of the science. There is also the fact that many scientists have experience of developing their own software, albeit in a very restricted setting, leading them to have unrealistic expectations about software development in a different setting. In this paper, we explore the challenges facing scientific software developers focusing especially on molecular biology. We claim that the nature and practice of molecular biology is quite different from that of the physical sciences and pose different problems to software developers. We do not claim that this paper is the last word on the topic but hope that it serves as the inspiration for further debate

Computational steering of a multi-objective genetic algorithm using a PDA

The execution process of a genetic algorithm typically involves some trial-and-error. This is due to the difficulty in setting the initial parameters of the algorithm – especially when little is known about the problem domain. The problem is magnified when applied to multi-objective optimisation, as care is needed to ensure that the final population of candidate solutions is representative of the trade-off surface. We propose a computational steering system that allows the engineer to interact with the optimisation routine during execution. This interaction can be as simple as monitoring the values of some parameters during the execution process, or could involve altering those parameters to influence the quality of the solutions produce by the optimisation process

Data as a Service (DaaS) for sharing and processing of large data collections in the cloud

Data as a Service (DaaS) is among the latest kind of services being investigated in the Cloud computing community. The main aim of DaaS is to overcome limitations of state-of-the-art approaches in data technologies, according to which data is stored and accessed from repositories whose location is known and is relevant for sharing and processing. Besides limitations for the data sharing, current approaches also do not achieve to fully separate/decouple software services from data and thus impose limitations in inter-operability. In this paper we propose a DaaS approach for intelligent sharing and processing of large data collections with the aim of abstracting the data location (by making it relevant to the needs of sharing and accessing) and to fully decouple the data and its processing. The aim of our approach is to build a Cloud computing platform, offering DaaS to support large communities of users that need to share, access, and process the data for collectively building knowledge from data. We exemplify the approach from large data collections from health and biology domains.Peer ReviewedPostprint (author's final draft

Steering in computational science: mesoscale modelling and simulation

This paper outlines the benefits of computational steering for high performance computing applications. Lattice-Boltzmann mesoscale fluid simulations of binary and ternary amphiphilic fluids in two and three dimensions are used to illustrate the substantial improvements which computational steering offers in terms of resource efficiency and time to discover new physics. We discuss details of our current steering implementations and describe their future outlook with the advent of computational grids.Comment: 40 pages, 11 figures. Accepted for publication in Contemporary Physic