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.
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/.
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.
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.
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.
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.
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.