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

Difficult phylogenetic questions: more data, maybe; better methods, certainly

Contradicting the prejudice that endosymbiosis is a rare phenomenon, Husník and co-workers show in BMC Biology that bacterial endosymbiosis has occured several times independently during insect evolution. Rigorous phylogenetic analyses, in particular using complex models of sequence evolution and an original site removal procedure, allow this conclusion to be established after eschewing inference artefacts that usually plague the positioning of highly divergent endosymbiont genomic sequences

Structure and evolution of the Gulf of Lions: The Sardinia seismic experiment and the GOLD (Gulf of Lions Drilling) project

International audienceThe study of the deep structure and evolution of passive continental margins is important for the understanding of rifting processes and the formation of associated sedimentary basins. Since the classical models of McKenzie (1978) and Wernicke (1985), understanding how passive continental margins form, that is to say mainly the way that continental lithosphere is thinned leading to subsidence, remains one of the main challenges in the Earth sciences. Many recent observations and discoveries have modified our basic views of margin formation. The conservational models paradigm (i.e., simple shear, pure shear, or polyphase models), which exclude exchanges between lower continental crust and upper mantle and which are usually proposed to explain lithospheric stretching and consequent crustal thinning of passive continental margins, fail to completely explain all these observations. Furthermore, these models imply a large amount of horizontal movement, movements not observed in the field. In consequence, new concepts need to be built and tested

Collaborative information seeking with ant colony ranking in real-time

In this paper we propose a new ranking algorithm based on Swarm Intelligence, more specifically on the Ant Colony Optimization technique, to improve search engines’ performances and reduce the information overload by exploiting users’ collective behavior. We designed an online evaluation involving end users to test our algorithm in a real-world scenario dealing with informational queries. The development of a fully working prototype – based on the Wikipedia search engine – demonstrated promising preliminary results

Mathematical practice, crowdsourcing, and social machines

The highest level of mathematics has traditionally been seen as a solitary endeavour, to produce a proof for review and acceptance by research peers. Mathematics is now at a remarkable inflexion point, with new technology radically extending the power and limits of individuals. Crowdsourcing pulls together diverse experts to solve problems; symbolic computation tackles huge routine calculations; and computers check proofs too long and complicated for humans to comprehend. Mathematical practice is an emerging interdisciplinary field which draws on philosophy and social science to understand how mathematics is produced. Online mathematical activity provides a novel and rich source of data for empirical investigation of mathematical practice - for example the community question answering system {\it mathoverflow} contains around 40,000 mathematical conversations, and {\it polymath} collaborations provide transcripts of the process of discovering proofs. Our preliminary investigations have demonstrated the importance of "soft" aspects such as analogy and creativity, alongside deduction and proof, in the production of mathematics, and have given us new ways to think about the roles of people and machines in creating new mathematical knowledge. We discuss further investigation of these resources and what it might reveal. Crowdsourced mathematical activity is an example of a "social machine", a new paradigm, identified by Berners-Lee, for viewing a combination of people and computers as a single problem-solving entity, and the subject of major international research endeavours. We outline a future research agenda for mathematics social machines, a combination of people, computers, and mathematical archives to create and apply mathematics, with the potential to change the way people do mathematics, and to transform the reach, pace, and impact of mathematics research.Comment: To appear, Springer LNCS, Proceedings of Conferences on Intelligent Computer Mathematics, CICM 2013, July 2013 Bath, U

Embalmed heads of the Celtic Iron Age in the south of France

Ancient texts described that one of the most impressive ritual practices of the Celts during the Iron Age was to remove the heads of enemies killed in battle and to embalm them for display in front of the victors dwellings. An archaeological settlement excavation site in Le Cailar, in southern France, has revealed a considerable number of examples of this practice. It was documented by Classical authors and later by the archaeological recording of iconographic representations and skeletal remains of human heads. Weapons were also exhibited alongside the severed heads. Here we report the results of chemical investigations for the characterization of the biomarkers of embalming that are likely to be present in eleven fragments of these human cranial remains. These results may lead to answers to some of the archaeometric questions related to the subject of embalming in 3rd century BC Transalpine Gaul, thus advancing the knowledge of these ritual practices, documented by Greek Classical authors as part of the wider research into the proto-historic societies of the Mediterranean coastal region

A Geological Itinerary Through the Southern Apennine Thrust-Belt (Basilicata—Southern Italy)

Open access via Springer Compact AgreementPeer reviewedPublisher PD

CaGrid Workflow Toolkit: A taverna based workflow tool for cancer grid

SOFTWAR