We present a software infrastructure that embeds physical hosts in a simulated network. Aiming to create a large-scale real-time virtual network testbed, our real-time interactive simulation approach combines the advantages of both simulation and emulation, by maintaining flexibility of the simulation models and increasing fidelity as real systems are included in the simulation. In our approach, real-world distributed applications and network services can run together with the real-time simulator; real packets are injected into the simulation and subject to the simulated network conditions computed as a result of both real and virtual traffic competing for network resources. A prototype of the proposed emulation infrastructure has been implemented based on virtual private network (VPN). One distinct advantage of our approach is that it does not require special hardware. Furthermore, it is flexible, secure, and scalable-attributes inherited directly from the VPN implementation. We conducted a set of preliminary experiments to assess the performance limitations of our emulation infrastructure. We also present an interesting case study to demonstrate the capability of our approach.

Workflow is an important enabling technology for eScience. Research into workflow systems for eScience has yielded several specialized workflow engines. In this paper we investigate the nature of scientific workflow and describe how an existing business workflow engine, Microsoft's BizTalk, can be adapted to support scientific workflow, and some advantages of doing this. We demonstrate how BizTalk is able to support scientific workflow through the implementation of two real bioinformatics workflows. These workflows are enacted through a novel Web based interface making them widely accessible.

Identification of nucleic acid sub-sequences within larger background sequences is a fundamental need of the biology community. The applicability correlates to research studies looking for homologous regions, diagnostic purposes and many other related activities. This paper serves to detail the approaches taken leading to sub-sequence identification through the use of hidden Markov models and associated scoring optimisations. The investigation of techniques for locating conserved basal promoter elements correlates to promoter thus gene identification techniques. The case study centred on the TATA box basal promoter element, as such the background is a gene sequence with the TATA box the target. Outcomes from the research conducted, highlights generic algorithms for sub-sequence identification, as such these generic processes can be transposed to any case study where identification of a target sequence is required. Paths extending from the work conducted in this investigation have led to the development of a generic framework for the future applicability of hidden Markov models to biological sequence analysis in a computational context.

Abraham Fraunce (1588, pp. 125r-139r), a lawyer of Gray's Inn, proposed the earliest map of case reasoning, using Plowden's report of the Exchequer case of Earl of Northumberland (1567). In 29 pages of diagrams, he set out the legal logic components of (1) the arguments of the opposing parties, namely Queen Elizabeth I and the Earl and (2) the judgment of the Court. The original work, written in Norman French with some Latin, was translated by Sybil Jack (2002). An extract of the translation, here published for the first time, indicates that Fraunce was a forerunner of legal knowledge engineering. The Earl's case diagrams are not unlike the extensive structure of the Latent Damage Law legal advice tree constructed by Capper and Susskind (1988, p72) four hundred years later.