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

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

Development of a biomechanical energy harvester

© 2009 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

The effects of exercise-induced muscle damage on endurance performance

It is well documented that engaging in resistance exercise can lead to further improvements in endurance performance. Whilst, not fully understood, it is speculated that increased motor unit recruitment, improved muscle coordination and enhanced utilisation of stored elastic energy after resistance-based exercise improves exercise economy. Nevertheless, while prolonged exposure to resistance training improves endurance performance in the long-term, a consequence of such training when unaccustomed is the appearance of exercise-induced muscle damage (EIMD). Exercise-induced muscle damage is well known to affect athletic performance requiring muscular strength and power; however, its effects on markers of endurance exercise are unclear. Therefore, the aim of this thesis was to investigate the effects of EIMD on endurance performance, with an emphasis on the physiological (oxygen uptake; , minute ventilation; ), metabolic (blood lactate; [La]), perceptual (rating of perceived exertion; RPE) and kinematic (stride length; SL, stride frequency; SF) responses during sub-maximal endurance exercise

An iterative identification procedure for dynamic modeling of biochemical networks

<p>Abstract</p> <p>Background</p> <p>Mathematical models provide abstract representations of the information gained from experimental observations on the structure and function of a particular biological system. Conferring a predictive character on a given mathematical formulation often relies on determining a number of non-measurable parameters that largely condition the model's response. These parameters can be identified by fitting the model to experimental data. However, this fit can only be accomplished when identifiability can be guaranteed.</p> <p>Results</p> <p>We propose a novel iterative identification procedure for detecting and dealing with the lack of identifiability. The procedure involves the following steps: 1) performing a structural identifiability analysis to detect identifiable parameters; 2) globally ranking the parameters to assist in the selection of the most relevant parameters; 3) calibrating the model using global optimization methods; 4) conducting a practical identifiability analysis consisting of two (<it>a priori </it>and <it>a posteriori</it>) phases aimed at evaluating the quality of given experimental designs and of the parameter estimates, respectively and 5) optimal experimental design so as to compute the scheme of experiments that maximizes the quality and quantity of information for fitting the model.</p> <p>Conclusions</p> <p>The presented procedure was used to iteratively identify a mathematical model that describes the NF-<it>κ</it>B regulatory module involving several unknown parameters. We demonstrated the lack of identifiability of the model under typical experimental conditions and computed optimal dynamic experiments that largely improved identifiability properties.</p