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.
5189033
Routing in grid graphs by cutting planes
In this paper we study the following problem, which we call the weighted routing problem. Let be given a graphG = (V, E) with non-negative edge weightswe ∈ ℝ+ and letN,N ≥ 1, be a list of node sets. The weighted routing problem consists in finding mutually disjoint edge setsS1,...,SN such that, for eachk ∈ {1, ...,N}, the subgraph (V(Sk),Sk) contains an [s, t]-path for alls, t ∈ Tk and the sum of the weights of the edge sets is minimal. Our motivation for studying this problem arises from the routing problem in VLSI-design, where given sets of points have to be connected by wires. We consider the weighted routing problem from a polyhedral point of view. We define an appropriate polyhedron and try to (partially) describe this polyhedron by means of inequalities. We describe our separation algorithms for some of the presented classes of inequalities. Based on these separation routines we have implemented a branch and cut algorithm. Our algorithm is applicable to an important subclass of routing problems arising in VLSI-design, namely to switchbox routing problems where the underlying graph is a grid graph and the list of node sets is located on the outer face of the grid. We report on our computational experience with this class of problem instances.
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.
23372292
A Calculus for Schemas in Z
The popularity and flexibility of the Z notation can largely be attributed to its notion of schemas. We describe these schemas and illustrate their various common uses in Z. We also present a collection of logical laws for manipulating these schemas. These laws are capable of supporting reasoning about the Z schema calculus in its full generality. This is demonstrated by presenting some theorems about the removability of schemas from Z specifications, together with outline proofs. We survey briefly models against which this logical system may be proven sound, and other related logics for Z.
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/.
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.
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.