Biochemical network matching and composition

This paper looks at biochemical network matching and compositio

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

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

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/

A comprehensive evaluation of assembly scaffolding tools.

Background: Genome assembly is typically a two-stage process: contig assembly followed by the use of paired sequencing reads to join contigs into scaffolds. Scaffolds are usually the focus of reported assembly statistics; longer scaffolds greatly facilitate the use of genome sequences in downstream analyses, and it is appealing to present larger numbers as metrics of assembly performance. However, scaffolds are highly prone to errors, especially when generated using short reads, which can directly result in inflated assembly statistics. Results: Here we provide the first independent evaluation of scaffolding tools for second-generation sequencing data. We find large variations in the quality of results depending on the tool and dataset used. Even extremely simple test cases of perfect input, constructed to elucidate the behaviour of each algorithm, produced some surprising results. We further dissect the performance of the scaffolders using real and simulated sequencing data derived from the genomes of Staphylococcus aureus, Rhodobacter sphaeroides, Plasmodium falciparum and Homo sapiens. The results from simulated data are of high quality, with several of the tools producing perfect output. However, at least 10% of joins remains unidentified when using real data. Conclusions: The scaffolders vary in their usability, speed and number of correct and missed joins made between contigs. Results from real data highlight opportunities for further improvements of the tools. Overall, SGA, SOPRA and SSPACE generally outperform the other tools on our datasets. However, the quality of the results is highly dependent on the read mapper and genome complexity

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

Heterogeneous oxidation of nitrite anion by gas-phase ozone in an aqueous droplet levitated by laser tweezers (optical trap):is there any evidence for enhanced surface reaction?

The oxidation of nitrite anion within an aqueous atmospheric droplet may be a sink for HONO in the lower atmosphere. An optical trap with Raman spectroscopy is used to demonstrate that the oxidation of aqueous nitrite anion in levitated, micron sized, aqueous droplets by gas-phase ozone is consistent with bulk aqueous phase kinetics and diffusion. There is no evidence of an enhanced or retarded reaction at the droplet surface at the concentrations used in the experiment or likely to be found in the atmosphere. The oxidation of nitrite in an aqueous droplet by gas phase ozone does not cause the droplet to hydrodynamically change in size and demonstrates use of an optical trap as a wall-less reactor to measuring aqueous phase rate coefficients

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

Comparison of stimulation patterns for FES-cycling using measures of oxygen cost and stimulation cost

<b>Aim</b><p></p> The energy efficiency of FES-cycling in spinal cord injured subjects is very much lower than that of normal cycling, and efficiency is dependent upon the parameters of muscle stimulation. We investigated measures which can be used to evaluate the effect on cycling performance of changes in stimulation parameters, and which might therefore be used to optimise them. We aimed to determine whether oxygen cost and stimulation cost measurements are sensitive enough to allow discrimination between the efficacy of different activation ranges for stimulation of each muscle group during constant-power cycling. <p></p> <b>Methods</b><p></p> We employed a custom FES-cycling ergometer system, with accurate control of cadence and stimulated exercise workrate. Two sets of muscle activation angles (“stimulation patterns”), denoted “P1” and “P2”, were applied repeatedly (eight times each) during constant-power cycling, in a repeated measures design with a single paraplegic subject. Pulmonary oxygen uptake was measured in real time and used to determine the oxygen cost of the exercise. A new measure of stimulation cost of the exercise is proposed, which represents the total rate of stimulation charge applied to the stimulated muscle groups during cycling. A number of energy-efficiency measures were also estimated. <p></p> <b>Results</b><p></p> Average oxygen cost and stimulation cost of P1 were found to be significantly lower than those for P2 (paired <i>t</i>-test, <i>p</i> < 0.05): oxygen costs were 0.56 ± 0.03 l min<sup>−1</sup> and 0.61 ± 0.04 l min<sup>−1</sup>(mean ± S.D.), respectively; stimulation costs were 74.91 ± 12.15 mC min<sup>−1</sup> and 100.30 ± 14.78 mC min<sup>−1</sup> (mean ± S.D.), respectively. Correspondingly, all efficiency estimates for P1 were greater than those for P2. <p></p> <b>Conclusion</b><p></p> Oxygen cost and stimulation cost measures both allow discrimination between the efficacy of different muscle activation patterns during constant-power FES-cycling. However, stimulation cost is more easily determined in real time, and responds more rapidly and with greatly improved signal-to-noise properties than the ventilatory oxygen uptake measurements required for estimation of oxygen cost. These measures may find utility in the adjustment of stimulation patterns for achievement of optimal cycling performance. <p></p&gt

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