7379720
W Reconstructed
An early version of the Z Standard included the deductive systemW for reasoning about Z specifications. Later versions contain a different deductive system. In this paper we sketch a proof that W is relatively sound with respect to this new deductive system. We do this by demonstrating a semantic basis for a correspondence between the two systems, then showing that each of the inference rules ofW can be simulated as derived rules in the new system. These new rules are presented as tactics over the the inference rules of the new deductive system.
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.
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.
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.
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.
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.
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.
15221918
Maintaining the Identity of Dynamically Embodied Agents
Virtual agents are traditionally constrained in their embodiment, as they are restricted to one form of body. We propose allowing them to change their embodiment in order to expand their capabilities. This presents users with a number of difficulties in maintaining the identity of the agents, but these can be overcome by using identity cues, certain features that remain constant across embodiment forms. This paper outlines an experiment that examines these identity cues, and shows that they can be used to help address this identity problem.
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.