A Linked Data Approach to Sharing Workflows and Workflow Results

A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users

Dimensional analysis using toric ideals: Primitive invariants

© 2014 Atherton et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Classical dimensional analysis in its original form starts by expressing the units for derived quantities, such as force, in terms of power products of basic units M, L, T etc. This suggests the use of toric ideal theory from algebraic geometry. Within this the Graver basis provides a unique primitive basis in a well-defined sense, which typically has more terms than the standard Buckingham approach. Some textbook examples are revisited and the full set of primitive invariants found. First, a worked example based on convection is introduced to recall the Buckingham method, but using computer algebra to obtain an integer K matrix from the initial integer A matrix holding the exponents for the derived quantities. The K matrix defines the dimensionless variables. But, rather than this integer linear algebra approach it is shown how, by staying with the power product representation, the full set of invariants (dimensionless groups) is obtained directly from the toric ideal defined by A. One candidate for the set of invariants is a simple basis of the toric ideal. This, although larger than the rank of K, is typically not unique. However, the alternative Graver basis is unique and defines a maximal set of invariants, which are primitive in a simple sense. In addition to the running example four examples are taken from: a windmill, convection, electrodynamics and the hydrogen atom. The method reveals some named invariants. A selection of computer algebra packages is used to show the considerable ease with which both a simple basis and a Graver basis can be found.The third author received funding from Leverhulme Trust Emeritus Fellowship (1-SST-U445) and United Kingdom EPSRC grant: MUCM EP/D049993/1

Flow Control with (Min,+) Algebra

According to the theory of Network Calculus based on the (min,+) algebra, analysis and measure of worst-case performance in communication networks can be made easily. In this context, this paper deals with traffic regulation and performance guarantee of a network i.e. with flow control. At first, assuming that a minimum service provided by a network is known, we aim at finding the constraint over the input flow in order to respect a maximal delay or backlog. Then, we deal with the window flow control problem in the following manner: The data stream (from the source to the destination) and the acknowledgments stream (from the destination to the source) are assumed to be different and the service provided by the network is assumed to be known in an uncertain way, more precisely it is assumed to be in an interval. The results are obtained by considering the Residuation theory which allows functions defined over idempotent semiring to be inverted

Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5

Rab11 GTPases are involved in various cellular processes but their activation by guanine nucleotide exchange factors (GEFs) is not fully understood. Here, the authors present a structural and biochemical analysis of Rab11 bound to the GEF SH3BP5, providing insights how Rab-GEF specificity is achieved

A Repeated Measures Experiment of Green Exercise to Improve Self-Esteem in UK School Children

Exercising in natural, green environments creates greater improvements in adult's self-esteem than exercise undertaken in urban or indoor settings. No comparable data are available for children. The aim of this study was to determine whether so called 'green exercise' affected changes in self-esteem; enjoyment and perceived exertion in children differently to urban exercise. We assessed cardiorespiratory fitness (20 m shuttle-run) and self-reported physical activity (PAQ-A) in 11 and 12 year olds (n = 75). Each pupil completed two 1.5 mile timed runs, one in an urban and another in a rural environment. Trials were completed one week apart during scheduled physical education lessons allocated using a repeated measures design. Self-esteem was measured before and after each trial, ratings of perceived exertion (RPE) and enjoyment were assessed after completing each trial. We found a significant main effect (F (1,74), = 12.2, p<0.001), for the increase in self-esteem following exercise but there was no condition by exercise interaction (F (1,74), = 0.13, p = 0.72). There were no significant differences in perceived exertion or enjoyment between conditions. There was a negative correlation (r = -0.26, p = 0.04) between habitual physical activity and RPE during the control condition, which was not evident in the green exercise condition (r = -0.07, p = 0.55). Contrary to previous studies in adults, green exercise did not produce significantly greater increases in self-esteem than the urban exercise condition. Green exercise was enjoyed more equally by children with differing levels of habitual physical activity and has the potential to engage less active children in exercise. © 2013 Reed et al

Workflows for Quantitative Data Analysis in The Social Sciences

The background is given to how statistical analysis is used by quantitative social scientists. Developing statistical analyses requires substantial effort, yet there are important limitations in current practice. This has motivated the authors to create a more systematic and effective methodology with supporting tools. The approach to modelling quantitative data analysis in the social sciences is presented. Analysis scripts are treated abstractly as mathematical functions and concretely as web services. This allows individual scripts to be combined into high-level workflows. A comprehensive set of tools allows workflows to be defined, automatically validated and verified, and automatically implemented. The workflows expose opportunities for parallel execution, can define support for proper fault handling, and can be realised by non-technical users. Services, workflows and datasets can also be readily shared. The approach is illustrated with a realistic case study that analyses occupational position in relation to health