David Gilbert

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Concurrent constraint programming is classically based on asynchronous communication via a shared store. This paper presents new versions of the ask and tell primitives which features synchronicity. Our approach is based on the idea of telling new information just in the case that a concurrently running process is asking for it. The new primitives are shown(More)
  • David Gilbert, David Westheady, Juris Viksnaz, Janet Thorntonx
  • 2000
Overview We describe the design and implementation of a fast topology{based method for protein structure comparison. The approach uses the TOPS topological representation of protein structure, aligning two structures using a common discovered pattern and generating measure of distance derived from an insert score. Heavy use is made of a constraint-based(More)
In this paper we have formalised and studied a language for describing constrained patterns in biosequences. We have developed an e cient and elegant algorithm for nding a given pattern in a sequence. The e ciency of the algorithm is determined by the fact that it does not use backtracking unlike other algorithms for dealing with constrained patterns.
Crucial to glucose homoeostasis in humans, the hPDC (human pyruvate dehydrogenase complex) is a massive molecular machine comprising multiple copies of three distinct enzymes (E1-E3) and an accessory subunit, E3BP (E3-binding protein). Its icosahedral E2/E3BP 60-meric 'core' provides the central structural and mechanistic framework ensuring favourable E1(More)
We present the first computational kinetic model of polyamine metabolism in bloodstream-form Trypanosoma brucei, the causative agent of human African trypanosomiasis. We systematically extracted the polyamine pathway from the complete metabolic network while still maintaining the predictive capability of the pathway. The kinetic model is constructed on the(More)
The BRIDGES project is a UK e-Science project that provides grid based support for biomedical research into the genetics of hypertension – the Cardiovascular Functional Genomics Project (CFG). Its main goal is to provide an effective environment for CFG, and biomedical research in general, including access to integrated data, analysis and visualization,(More)
In this chapter we review techniques for sequence based pattern discovery and comparison, and show how these can be extended to RNA structures and abstract representations of protein structure at the fold level. We first define deterministic patterns over sequences and distinguish pattern matching from string comparison, reviewing the use of dynamic(More)