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

Economic modelling using constraint logic programming

This paper investigates the use of constraint logic programming (CLP) in economic modelling through the design and implementation of two economic models. The first model, the Desai- Henry model contains only linear equations while the second model, constructed by the author, contains non-linear elements. In order to implement the second model, a non-linear constraint solver was constructed. This was necessary because, although CLP is a very powerful programming paradigm, currently available implementations lack any on-linear constraint solving mechanisms

A Monte Carlo model checker for probabilistic LTL with numerical constraints

We define the syntax and semantics of a new temporal logic called probabilistic LTL with numerical constraints (PLTLc). We introduce an efficient model checker for PLTLc properties. The efficiency of the model checker is through approximation using Monte Carlo sampling of finite paths through the model’s state space (simulation outputs) and parallel model checking of the paths. Our model checking method can be applied to any model producing quantitative output – continuous or stochastic, including those with complex dynamics and those with an infinite state space. Furthermore, our offline approach allows the analysis of observed (real-life) behaviour traces. We find in this paper that PLTLc properties with constraints over free variables can replace full model checking experiments, resulting in a significant gain in efficiency. This overcomes one disadvantage of model checking experiments which is that the complexity depends on system granularity and number of variables, and quickly becomes infeasible. We focus on models of biochemical networks, and specifically in this paper on intracellular signalling pathways; however our method can be applied to a wide range of biological as well as technical systems and their models. Our work contributes to the emerging field of synthetic biology by proposing a rigourous approach for the structured formal engineering of biological systems

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

Interaction of agents and environments

A new abstract model of interaction between agents and environments considered as objects of different types is introduced. Agents are represented by means of labelled transition systems considered up to bisimilarity. The equivalence of agents is characterised in terms of an algebra of behaviours which is a continuous algebra with approximation and two operations: nondeterministic choice and prefixing. Environments are introduced as agents supplied with an insertion function which takes the behaviour of an agent and the behaviour of an environment as arguments and returns the new behaviour of an environment. Arbitrary continuous functions can be used as insertion functions, and we use functions defined by means of rewriting logic as computable ones. The transformation of environment behaviours defined by the insertion function also defines a new type of agent equivalence--- insertion equivalence. Two behaviours are insertion equivalent if they define the same transformation of an environment. The properties of this equivalence are studied. Three main types of insertion functions are used to develop interesting applications: one-step insertion, head insertion, and look-ahead insertion functions

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

Determination of the Optimal Conditions for Bovine Serum Albumin Surface Enhanced Raman Scattering on Silver Colloids

Bovine serum albumin (BSA) was analyzed using surface enhanced Raman scattering (SERS) to find the optimal conditions to observe BSA with SERS. Colloidal silver, Na2SO4, and BSA were mixed together at varying pHs and concentrations to obtain multiple spectra.The most favorable conditions using SERS for BSA were 500ug/mL and pH 4.The spectrum under those conditions showed the most intense and discernible peaks and the alpha helical secondary structure was very distinct at 1297 cm-1. SERS can be used for label free detection of proteins, thus finding the best conditions to obtain spectra using this technique may be very beneficial to proteomic research

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