FURY: Fuzzy unification and resolution based on edit distance

We present a theoretically founded framework for fuzzy unification and resolution based on edit distance over trees. Our framework extends classical unification and resolution conservatively. We prove important properties of the framework and develop the FURY system, which implements the framework efficiently using dynamic programming. We evaluate the framework and system on a large problem in the bioinformatics domain, that of detecting typographical errors in an enzyme name databas

Timetabling in constraint logic programming

In this paper we describe the timetabling problem and its solvability in a Constraint Logic Programming Language. A solution to the problem has been developed and implemented in ECLiPSe, since it deals with finite domains, it has well-defined interfaces between basic building blocks and supports good debugging facilities. The implemented timetable was based on the existing, currently used, timetables at the School of Informatics at out university. It integrates constraints concerning room and period availability

A novel method for comparing topological models of protein structures enhanced with ligand information

This article is available open access through the publisher’s website through the link below. Copyright @ 2008 The Authors.We introduce TOPS+ strings, a highly abstract string-based model of protein topology that permits efficient computation of structure comparison, and can optionally represent ligand information. In this model, we consider loops as secondary structure elements (SSEs) as well as helices and strands; in addition we represent ligands as first class objects. Interactions between SSEs and between SSEs and ligands are described by incoming/outgoing arcs and ligand arcs, respectively; and SSEs are annotated with arc interaction direction and type. We are able to abstract away from the ligands themselves, to give a model characterized by a regular grammar rather than the context sensitive grammar of the original TOPS model. Our TOPS+ strings model is sufficiently descriptive to obtain biologically meaningful results and has the advantage of permitting fast string-based structure matching and comparison as well as avoiding issues of Non-deterministic Polynomial time (NP)-completeness associated with graph problems. Our structure comparison method is computationally more efficient in identifying distantly related proteins than BLAST, CLUSTALW, SSAP and TOPS because of the compact and abstract string-based representation of protein structure which records both topological and biochemical information including the functionally important loop regions of the protein structures. The accuracy of our comparison method is comparable with that of TOPS. Also, we have demonstrated that our TOPS+ strings method out-performs the TOPS method for the ligand-dependent protein structures and provides biologically meaningful results. Availability: The TOPS+ strings comparison server is available from http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/topsplus.html.University of Glasgo

Effects of Fermion Flavor on Exciton Condensation in Double Layer Systems

We use fermionic path integral quantum Monte Carlo to study the effects of fermion flavor on the physical properties of dipolar exciton condensates in double layer systems. We find that by including spin in the system weakens the effective interlayer interaction strength, yet this has very little effect on the Kosterlitz-Thouless transition temperature. We further find that, to obtain the correct description of screening, it is necessary to account for correlation in both the interlayer and intralayer interactions. We show that while the excitonic binding cannot completely surpress screening by additional fermion flavors, their screening effectiveness is reduced leading to a much higher transition temperatures than predicted with large-N analysis.Comment: 4 pages, 3 figure

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks