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.
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.
26464031
A Taxonomy of Web Services Using CSP
Terms such as conversational and stateless are widely used in the taxonomy of web services. We give formal definitions of these terms using the CSP process algebra. Within this framework we also define the notion of Service-Oriented Architecture. These definitions are then used to prove important scalability properties of stateless services. The use of formalism should allow recent debates, concerning how and whether web services provide standardized access to state, to progress more rigorously.
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.
16635941
Packing Steiner trees: a cutting plane algorithm and computational results
In this paper we describe a cutting plane algorithm for the Steiner tree packing problem. We use our algorithm to solve some switchbox routing problems of VLSI-design and report on our computational experience. This includes a brief discussion of separation algorithms, a new LP-based primal heuristic and implementation details. The paper is based on the polyhedral theory for the Steiner tree packing polyhedron developed in our companion paper (this issue) and meant to turn this theory into an algorithmic tool for the solution of practical problems.
17355175
Packing Steiner Trees: Separation Algorithms
In this paper, we investigate separation problems for classes of inequalities valid for the polytope associated with the Steiner tree packing problem, a problem that arises, e.g., in very large-scale integration (VLSI) routing. The separation problem for Steiner partition inequalities is \NP-hard in general. We show that it can be solved in polynomial time for those instances that come up in switchbox routing. Our algorithm uses dynamic programming techniques. These techniques are also applied to the much more complicated separation problem for alternating cycle inequalities. In this case, we can compute in polynomial time, given some point $y$, a lower bound for the gap $\alpha-a^Ty$ over all alternating cycle inequalities $a^Tx\ge\alpha$. This gives rise to a very effective separation heuristic. A by-product of our algorithm is the solution of a combinatorial optimization problem that is interesting in its own right: find a shortest path in a graph where the "length" of a path is its usual length minus the length of its longest edge.
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/.
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.
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.