Biochemical network matching and composition

This paper looks at biochemical network matching and compositio

Composition of Biochemical Networks using Domain Knowledge

Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the possible solutions to the graph merge problem. We show that our XML graph merge solution performs well in practice and improves on the existing toolsets. This leads us into future work directions and the plan of research which will aim to implement graph merging primitives using domain knowledge to perform composition and decomposition on specific graphs in the biological domain

reSearch : enhancing information retrieval with images

Combining image and text search is an open research question. The main issues are what technologies to base this solution on, and what measures of relevance to employ. Our reSearch prototype mashes up papers indexed using information retrieval techniques (Terrier) with Google image search for faces and Google book search. The user can interactively employ query expansion with additional terms suggested by Terrier, and use those terms to expand both the text and image search. We test this solution with a selection of recent publications and queries concerning people engaged in research. We report on the effectiveness of this solution. It seems that the combination works to a large extent, as testified by our observations

Circular Ocean WP3.1: potential applications of 3D printing (3DP) in the recycling of fishing nets & ropes (FNR's)

Working paper for Circular Ocean, a three year project (2015-2018) that aims to inspire communities to realise the hidden economic opportunities of discarded fishing nets and ropes in the Northern Periphery and Arctic region. The Circular Ocean project is funded by the ERDF Interreg VB Northern Periphery and Arctic (NPA) Programme, under Priority Axis 2; Promoting Entrepeneurship to Realise the Potential of the Programme Area's Competitive Advantage

REAPR: a universal tool for genome assembly evaluation.

Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/

Circlator: automated circularization of genome assemblies using long sequencing reads

The assembly of DNA sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. Assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved. Here we present Circlator, the first tool to automate assembly circularization and produce accurate linear representations of circular sequences. Using Pacific Biosciences and Oxford Nanopore data, Circlator correctly circularized 26 of 27 circularizable sequences, comprising 11 chromosomes and 12 plasmids from bacteria, the apicoplast and mitochondrion of Plasmodium falciparum and a human mitochondrion. Circlator is available at http://sanger-pathogens.github.io/circlator/

Designing for users: Online informaiton literacy in the Middle East

Librarians from Zayed University in the United Arab Emirates (UAE) report on an empirical evaluation of the relevance and value of Infoasis (http://www.zu.ac.a /infoasis), a Webbased information literacy tutorial developed and tailored to the Arab student population of the Emirates. After the successful implementation of this project, questions arose about the value of maintaining Infoasis, given the time intensive nature of this activity. Was the tutorial relevant and useful to students? Was it being used by students, and what factors contributed to the engagement (or not) of students with the tutorial? Survey results concluded that students found the tutorial both relevant and useful to their studies and that the design features tailored to the needs of the undergraduate Arab population were effective in ensuring usability. Reasons for poor usage of Infoasis outside the classroom are discussed

Bayesian Calibration Tool

Fitting a model to data is common practice in many fields of science. The models may contain unknown parameters and often, the goal is to obtain good estimates of them. A variety of methods have been developed for this purpose. They often differ in complexity, efficiency and accuracy and some may have very limited applications. Bayesian inference methods have recently become popular for the purpose of calibrating model\u27s parameters. The way they treat unknown quantities is completely different from any classical methods. Even though the unknown quantity is a constant, it is treated as a random variable and the desired outcome is it\u27s probability distribution. Good estimates and confidence intervals can then be easily produced from probability distributions. Anohter important feature of Bayesian inference is the ability to include prior knowledge in the calculations. However, Bayesian inference has to be done computationally as it involves solving multidimensional integrals. The Bayesian Calibration tool is an easy-to-use, well documented tool to efficiently carry out the calculations of the calibration process. The tool is open-source and uses fast Markov Chain Monte Carlo (MCMC) algorithms. The tool is run on nanoHUB, making it easily accessible without installing any software, etc. Given data and a model, the tool performs MCMC simulation of the model and returns the Bayesian posterior probability distributions of the model\u27s unknown parameters

A potential library for primary MFL pedagogy: the case of Young Pathfinders

As readers of this journal will know very well, 2010 will see all KS2 (ages 7-11) pupils in England entitled to learn a modern foreign language in normal curriculum time. This development of the commitment to primary language learning should provide an excellent opportunity and experience for pupils, whilst at the same time requiring some radical changes for many teachers, schools and much of the wider language learning community. Recent research has indicated general trends suggesting an increase in primary languages already, in anticipation of this development and even beforehand. One of the most recent studies indicates that 43% of primary children currently learn a foreign language at KS2, either in class or as an extra-curricular activity, although the extent of this learning varies considerably (Driscoll, Jones and Macrory, 2004). It has also been suggested (Muijs et al, 2005) that there are certain aspects of the process that will be particularly demanding if the challenge of providing this entitlement are to be met