37164715
The Cogito Development System
The Cogito system provides comprehensive support for the development of specifications written in the Sum language (a modular extension of Z). The tool-set provides technology to aid in the construction, analysis and development of Sum specifications. Ada code is the final result of a development in Cogito.
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.
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.
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.
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.
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.
2188414
Agents in bioinformatics, computational and systems biology
The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.
23466253
The CATH Database provides insights into protein structure/function relationships
We report the latest release (version 1.4) of the CATH protein domains database (http://www.biochem.ucl.ac.uk/bsm/cath). This is a hierarchical classification of 13 359 protein domain structures into evolutionary families and structural groupings. We currently identify 827 homologous families in which the proteins have both structual similarity and sequence and/or functional similarity. These can be further clustered into 593 fold groups and 32 distinct architectures. Using our structural classification and associated data on protein functions, stored in the database (EC identifiers, SWISS-PROT keywords and information from the Enzyme database and literature) we have been able to analyse the correlation between the 3D structure and function. More than 96% of folds in the PDB are associated with a single homologous family. However, within the superfolds, three or more different functions are observed. Considering enzyme functions, more than 95% of clearly homologous families exhibit either single or closely related functions, as demonstrated by the EC identifiers of their relatives. Our analysis supports the view that determining structures, for example as part of a 'structural genomics' initiative, will make a major contribution to interpreting genome data.
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.
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/.
14479325
Bus catcher: a context sensitive prototype system for public transportation users
In this paper we describe the architectural andfunctional characteristics of Bus Catcher, a contextsensitive prototype system for public transportation users.Bus Catcher assists mobile users in planning their busrides by providing timely and accurate information aboutcurrent bus locations and estimated arrival times. Acomplete report on the implementation together with apreliminary evaluation of the system is provided in thispaper.