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

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

Transient analysis and synthesis of linear circuits using constraint logic programming

In this paper describes the design of a transient analysis program for linear circuits and its implementation in a Constraint Logic Programming language, CLP(R). The transient analysis program parses the input circuit description into a network graph, analyses its semantic correctness and then performs the transient analysis. The test results show that the program is at least 97% accurate when run at two decimal places. We have also compared the performance of our program with a commercial package implemented in an imperative language. The advantages of implementing the analysis program in a CLP language include: quick construction and ease of maintenance. We also report on the synthesis of generation of a circuit with given transient characteristics

Interactive visualisation and exploration of biological data

International audienceno abstrac

Relations between extensional tectonics and magmatism within the Southern Oklahoma aulacogen

Variations in the geometry, distribution and thickness of Cambrian igneous and sedimentary units within southwest Oklahoma are related to a late Proterozoic - early Paleozoic rifting event which formed the Southern Oklahoma aulacogen. These rock units are exposed in the Wichita Mountains, southwest Olkahoma, located on the northern margin of a Proterozoic basin, identified in the subsurface by COCORP reflection data. Overprinting of the Cambrian extensional event by Pennyslvanian tectonism obsured the influence of pre-existing basement structures and contrasting basement lithologies upon the initial development of the aulacogen

Transformations between HCLP and PCSP

We present a general methodology for transforming between HCLP and PCSP in both directions. HCLP and PCSP each have advantages when modelling problems, and each have advantages when implementing models and solving them. Using the work presented in this paper, the appropriate paradigm can be used for each of these steps, with a meaning-preserving transformation in between if necessary

A process algebra for synchronous concurrent constraint programming

Concurrent constraint programming is classically based on asynchronous communication via a shared store. This paper presents new version 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. An operational and an algebraic semantics are defined. The algebraic semantics is proved to be sound and complete with respect to a compositional operational semantics which is also presented in the paper

Developing a new business model for enabling research - the case of the ACPFG in Australia

Publisher's postprint archived as permitted by publisher.The way in which companies, research centres and educational institutions are organised and structured may provide a competitive advantage for commercialisation, in particular if companies are dependent on the deployment of complementary assets and capabilities by third parties. This paper presents the case of the Australian Centre for Plant Functional Genomics (ACPFG), a private agricultural biotechnology (agbiotech) company specialising in early stage Research and Development (R&D) to produce superior adapted cereal varieties, tolerant to abiotic stress conditions such as drought, frost, salt, or mineral toxicity, all of which have a direct and negative impact on plant growth and crop productivity. The organisational structure of the company has been influenced and shaped by Government policy, shareholders expectations and trends in the agbiotech industrial organisation. It has proved attractive to potential alliance partners for collaborative R&D and commercialisation. We present the ACPFG as a new business model to fund basic research and facilitate technology transfer.Stephanie C. Agius, David Corkindale, Antonio G. Dottore, Michael Gilber

Analysis of signalling pathways using the prism model checker

We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable