14876854
Security principles for public-resource modeling research
Large-scale distributed computing projects have many security concerns due to their public and often "open" nature. Climateprediction.net (CPDN) is taking the concept of public-resource, high-throughput grid computing a stage further, by using it for a major piece of modeling research. The aim is to harness the spare CPU cycles of potentially millions of individual users' PCs to run a massive ensemble of climate simulations. In doing so it has been faced with a range of security and integrity issues beyond those encountered by previous projects but likely also to confront similar initiatives in the future. This paper introduces the project and its software architecture, and outlines a threat model for such situations, including threats to participants, threats to the experiment and threats to other stakeholders. It goes on to discuss how these threats have been addressed, with the procedures presented expected to form a valuable foundation for an increasing number of similar projects.
265154
A Set-Theoretic Model for Real-Time Specification and Reasoning
Timed-trace formalisms have emerged as a powerful method for specifying and reasoning about concurrent real-time systems. We present a simple variant which builds methodically on set theory, and is thus suitable for use by programmers with little formal methods experience.
34718551
Encoding W: A Logic for Z in 2OBJ
A prototype proof system for “\(\mathcal{W}\): A Logic for Z” has been produced using the 2OBJ metalogical theorem-prover. 2OBJ permits an encoding which is very similar in structure to that of \(\mathcal{W}\), and the details are presented here. Like \(\mathcal{W}\)the encoding assumes that all its inputs are well-typed. The structure of the encoding is enhanced by a meta-rule on the lifting of proof rules and tactics. There is some discussion of how tactics can make \(\mathcal{W}\)more easily usable.
6469757
Teaching Formal Methods in Context
The Software Engineering Programme at Oxford teaches formal methods as an integral part of its programme of professional education in software engineering. This paper explains how the methods are taught—in the context of emerging trends in software development, and in the context of existing practice—and how their use is promoted through course design and motivating examples.
14174107
Lifting in Z
Formal notations such as Z provide powerful support for writing clear specifications, and for undertaking proofs of properties of those specifications. In this paper, we explore one particular style of specification, with applications in control theory and real-time specification. The notation we define permits the accurate description of concepts in these fields without significant overhead or notational clutter. This notation has long been used by practitioners in these fields; we demonstrate that it may be defined within Draft Standard Z, and that the resulting specifications are amenable to proof.
14876206
E-science experiences: software engineering practice and the EU DataGrid
The conduct of collaborative scientific study mediated by the internet -e-science - is giving rise to a new type of large distributed software project. This paper reports initial experiences of one such project: the European DataGrid. We record observations about the intended lifecycle and process, compared with actual practice. The paper explores the applicability of current software development practices from academic, commercial, and open source sectors in the context of such Grid projects.
16348358
Agent Chameleons: Virtual Agents Real Intelligence
Agent Chameleons provides virtual agents powered by real intelligence, delivering next generation autonomic entities that can seamlessly migrate, mutate and evolve on their journey between and within physical and digital information spaces.
33375279
Mapping PDB chains to UniProtKB entries
MOTIVATION
UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file.


RESULTS
We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping.


AVAILABILITY
The resource may be queried interactively or downloaded from http://www.bioinf.org.uk/pdbsws/.
18494896
The steiner tree packing problem in VLSI design
In this paper we describe several versions of the routing problem arising in VLSI design and indicate how the Steiner tree packing problem can be used to model these problems mathematically. We focus on switchbox routing problems and provide integer programming formulations for routing in the knock-knee and in the Manhattan model. We give a brief sketch of cutting plane algorithms that we developed and implemented for these two models. We report on computational experiments using standard test instances. Our codes are able to determine optimum solutions in most cases, and in particular, we can show that some of the instances have no feasible solution if Manhattan routing is used instead of knock-knee routing.
5379517
Packing Steiner Trees: Further Facets
Abstract In this paper we continue the investigations in [3] for the Steiner tree packing polyhedron. We present several new classes of valid inequalities and give sufficient (and necessary) conditions for these inequalities to be facet-definining. It is intended to incorporate these inequalities into an existing cutting plane algorithm that is applicable to practical problems arising in the design of electronic curcuits.
34039430
A model of information systems development project performance
. Performance in information systems development (ISD) projects can be critical to business success. But, while project performance has been the subject of much debate, there has been little empirical research into its determinants. A survey of IS projects in the UK and New Zealand is analysed to test hypotheses concerning performance in terms of both project completion and budget (time-cost) variances. Subsequently, a secondary analysis of the findings is used to build a more complete empirical model of project performance. The paper helps to develop the theory of IS development project performance and also has significant implications for practice. Discussion of the findings highlights the importance of project team dynamics, risk management, senior management support for strategic projects and user participation in ensuring successful IS project performance.