EPSRC Institutional Sponsorship 2012-13 – Loughborough University: final report

EPSRC Institutional Sponsorship 2012-13 – Loughborough University: final repor

Extracting and re-using research data from chemistry e-theses: the SPECTRa-T project

Scientific e-theses are data-rich resources, but much of the information they contain is not readily accessible. For chemistry, the SPECTRa-T project has addressed this problem by developing data-mining techniques to extract experimental data, creating RDF (Resource Description Framework) triples for exposure to sophisticated Semantic Web searches. We used OSCAR3, an Open Source chemistry text-mining tool, to parse and extract data from theses in PDF, and from theses in Office Open XML document format. Theses in PDF suffered data corruption and a loss of formatting that prevented the identification of chemical objects. Theses in .docx yielded semantically rich SciXML that enabled the additional extraction of associated data. Chemical objects were placed in a data repository, and RDF triples deposited in a triplestore. Data-mining from chemistry e-theses is both desirable and feasible; but the use of PDF, the de facto format standard for deposit in most repositories, prevents the optimal extraction of data for semantic querying. In order to facilitate this, we recommend that universities also require deposition of chemistry e-theses in an XML document format. Further work is required to clarify the complex IPR issues and ensure that they do not become an unwarranted barrier to data extraction and re-use

CMLLite: a design philosophy for CML.

CMLLite is a collection of definitions and processes which provide strong and flexible validation for a document in Chemical Markup Language (CML). It consists of an updated CML schema (schema3), conventions specifying rules in both human and machine-understandable forms and a validator available both online and offline to check conformance. This article explores the rationale behind the changes which have been made to the schema, explains how conventions interact and how they are designed, formulated, implemented and tested, and gives an overview of the validation service.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Intermediate scattering function and quantum recoil in non-Markovian quantum diffusion

Exact expressions are derived for the intermediate scattering function (ISF) of a quantum particle diffusing in a harmonic potential and linearly coupled to a harmonic bath. The results are valid for arbitrary strength and spectral density of the coupling. The general, exact non-Markovian result is expressed in terms of the classical velocity autocorrelation function, which represents an accumulated phase during a scattering event. The imaginary part of the exponent of the ISF is proportional to the accumulated phase, which is an antisymmetric function of the correlation time $t$. The expressions extend previous results given in the quantum Langevin framework where the classical response of the bath was taken as Markovian. For a special case of non-Markovian friction, where the friction kernel decays exponentially in time rather than instantaneously, we provide exact results relating to unconfined quantum diffusion, and identify general features that allow insight to be exported to more complex examples. The accumulated phase as a function of the t has a universal gradient at the origin, depending only on the mass of the diffusing system particle. At large t the accumulated phase reaches a constant limit that depends only on the classical diffusion coefficient and is therefore independent of the detailed memory properties of the friction kernel. Non-Markovian properties of the friction kernel are encoded in the details of how the accumulated phase switches from its $t\rightarrow -\infty$ to its $t\rightarrow -\infty$ limit, subject to the constraint of the universal gradient. When memory effects are significant, the transition from one limit to the other becomes non-monotonic, owing to oscillations in the classical velocity autocorrelation. The result is interpreted in terms of a solvent caging effect, in which slowly fluctuating bath modes create transient wells for the system particle.PT thanks the EPSRC for doctoral funding under the award reference 1363145, which enabled the majority of the present work

Szegénység, társadalmi kirekesztés és társadalmi polarizáció, avagy: miért van szükség egy nemzetközi jóléti állam létrehozására

Az elmúlt, nagyjából ötven évben a konvencionális bölcsesség egyre csak azt szajkózta, hogy a gazdasági növekedés automatikusan csökkenti majd a szegénységet. Ez az álláspont nem tartható tovább. Az elkövetkező majd’ fél évszázad kilátásai szerint a világ legalapvetőbb problémája az lesz – s ebben teljes az egyetértés a nagy nemzetközi intézmények között, egyre inkább teszik magukévá ezt a véleményt az egyes kormányok is –, hogy a gazdagság és a szegénység egyre polarizáltabbnak mutatkozik meg, s hogy új prioritásokat kell kitűznünk magunk elé

A semantic Grid for molecular science

Proceedings of the 2003 UK e-Science All Hands Meeting, 31st August - 3rd September, Nottingham UKThe properties of molecules have very well defined semantics and allow the creation of a semantic GRID. Markup languages (CML - Chemical Markup Language) and dictionary-based ontologies have been designed to support a wide range of applications, including chemical supply, publication and the safety of compounds. Many properties can be computed by Quantum Mechanical (QM) programs and we have developed a "black-box" system based on XML wrappers for all components. This is installed on a Condor system on which we have computed properties for 250, 000 compounds. The results of this will be available in an OpenData/OpenSource peer-to-peer (P2P) system (WorldWide Molecular Matrix - WWMM)