Towards data grids for microarray expression profiles

The UK DTI funded Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) project developed a Grid infrastructure through which research into the genetic causes of hypertension could be supported by scientists within the large Wellcome Trust funded Cardiovascular Functional Genomics project. The BRIDGES project had a focus on developing a compute Grid and a data Grid infrastructure with security at its heart. Building on the work within BRIDGES, the BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project plans to provide an enhanced data Grid infrastructure to support richer queries needed for the discovery and analysis of microarray data sets, also based upon a fine-grained security infrastructure. This paper outlines the experiences gained within BRIDGES and outlines the status of the GEMEPS project, the open challenges that remain and plans for the future

Security-oriented data grids for microarray expression profiles

Microarray experiments are one of the key ways in which gene activity can be identified and measured thereby shedding light and understanding for example on biological processes. The BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project has developed an infrastructure which allows post-genomic life science researchers to ask and answer the following questions: who has undertaken microarray experiments that are in some way similar or relevant to mine; and how similar were these relevant experiments? Given that microarray experiments are expensive to undertake and may possess crucial information for future exploitation (both academically and commercially), scientists are wary of allowing unrestricted access to their data by the wider community until fully exploited locally. A key requirement is thus to have fine grained security that is easy to establish and simple (or ideally transparent) to use across inter-institutional virtual organisations. In this paper we present an enhanced security-oriented data Grid infrastructure that supports the definition of these kinds of queries and the analysis and comparison of microarray experiment results

Precise computer controlled positioning of robot end effectors using force sensors

A major problem in space applications of robotics and docking of spacecraft is the development of technology for automated precise positioning of mating components with smooth motion and soft contact. To achieve the above objective, a design method was developed for optimally placing the closed-loop poles of a discretized robotic control system at exact prescribed locations inside the unit circle of the complex z-plane. The design method combines the merits of the pole placement and the linear quadratic design approaches. The proposed design procedure is based on the assignment of one real eigenvalue or two complex conjugate (or real) eigenvalues at each design step. The method involves solutions of simple algebraic equations and this is considered to be efficient for on-line or off-line computations. Also, two methods for the linearization of the nonlinear model of a robotic manipulator were presented. Since automatic control of multi-degree freedom robotic manipulators involves high nonlinear equations of systems, a pilot project was proposed involving the control of a one-dimensional system. This simple system can be readily implemented for testing the concepts and algorithms

A systematic review of lesbian, gay, bisexual and transgender health in the West Midlands region of the UK compared to published UK research

It is estimated that approximately 3-8% of the UK population identify as lesbian, gay, bisexual or trans (LGBT). Until now, most health research on gay and bisexual men has been around HIV, AIDS and sexually transmitted diseases and for trans people has been on the transitioning process only. However, it has been apparent to the LGBT community that that there are a wide variety of other physical and mental health issues that are also important and that the proportion of gay and bisexual men who have HIV/AIDS is relatively small. Very little general LGBT health research has been published so far and there are very few health services that specifically address the general health concerns of the LGBT community. This systematic review presents all available research conducted in the West Midlands on LGBT health since 2000. Local health research is compared to UK national, peer reviewed and published LGBT health research in order to determine whether the local results are unusual compared to national LGBT data, and to routinely collected data on the UK population, where appropriate, in order to determine whether and where the LGBT population differ from the general population. Only UK research has been included because there was no previous UK specific systematic review so it was unclear how generalisable foreign research would be to the UK

The numerical solution of the Helmholtz equation for wave propagation problems in underwater acoustics

The Helmholtz Equation (-delta-K(2)n(2))u=0 with a variable index of refraction, n, and a suitable radiation condition at infinity serves as a model for a wide variety of wave propagation problems. A numerical algorithm was developed and a computer code implemented that can effectively solve this equation in the intermediate frequency range. The equation is discretized using the finite element method, thus allowing for the modeling of complicated geometrices (including interfaces) and complicated boundary conditions. A global radiation boundary condition is imposed at the far field boundary that is exact for an arbitrary number of propagating modes. The resulting large, non-selfadjoint system of linear equations with indefinite symmetric part is solved using the preconditioned conjugate gradient method applied to the normal equations. A new preconditioner is developed based on the multigrid method. This preconditioner is vectorizable and is extremely effective over a wide range of frequencies provided the number of grid levels is reduced for large frequencies. A heuristic argument is given that indicates the superior convergence properties of this preconditioner

On accuracy conditions for the numerical computation of waves

The Helmholtz equation (Delta + K(2)n(2))u = f with a variable index of refraction n, and a suitable radiation condition at infinity serves as a model for a wide variety of wave propagation problems. Such problems can be solved numerically by first truncating the given unbounded domain and imposing a suitable outgoing radiation condition on an artificial boundary and then solving the resulting problem on the bounded domain by direct discretization (for example, using a finite element method). In practical applications, the mesh size h and the wave number K, are not independent but are constrained by the accuracy of the desired computation. It will be shown that the number of points per wavelength, measured by (Kh)(-1), is not sufficient to determine the accuracy of a given discretization. For example, the quantity K(3)h(2) is shown to determine the accuracy in the L(2) norm for a second-order discretization method applied to several propagation models

A Spin-Orbit Alignment for the Hot Jupiter HATS-3b

We have measured the alignment between the orbit of HATS-3b (a recently discovered, slightly inflated Hot Jupiter) and the spin-axis of its host star. Data were obtained using the CYCLOPS2 optical-fiber bundle and its simultaneous calibration system feeding the UCLES spectrograph on the Anglo-Australian Telescope. The sky-projected spin-orbit angle of $\lambda = 3\pm25^{\circ}$ was determined from spectroscopic measurements of Rossiter-McLaughlin effect. This is the first exoplanet discovered through the HATSouth transit survey to have its spin-orbit angle measured. Our results indicate that the orbital plane of HATS-3b is consistent with being aligned to the spin axis of its host star. The low obliquity of the HATS-3 system, which has a relatively hot mid F-type host star, agrees with the general trend observed for Hot Jupiter host stars with effective temperatures $>6250$K to have randomly distributed spin-orbit angles.Comment: 13 pages. Accepted for publication in the Astrophysical Journa

Measurement of the Nodal Precession of WASP-33 b via Doppler Tomography

We have analyzed new and archival time series spectra taken six years apart during transits of the hot Jupiter WASP-33 b, and spectroscopically resolved the line profile perturbation caused by the Rossiter-McLaughlin effect. The motion of this line profile perturbation is determined by the path of the planet across the stellar disk, which we show to have changed between the two epochs due to nodal precession of the planetary orbit. We measured rates of change of the impact parameter and the sky-projected spin-orbit misalignment of $db/dt=-0.0228_{-0.0018}^{+0.0050}$ yr$^{-1}$ and $d\lambda/dt=-0.487_{-0.076}^{+0.089}$~$^{\circ}$ yr$^{-1}$, respectively, corresponding to a rate of nodal precession of $d\Omega/dt=0.373_{-0.083}^{+0.031}$~$^{\circ}$ yr$^{-1}$. This is only the second measurement of nodal precession for a confirmed exoplanet transiting a single star. Finally, we used the rate of precession to set limits on the stellar gravitational quadrupole moment of $9.4\times10^{-5}<J_2<6.1\times10^{-4}$.Comment: Published in ApJL. 5 pages, 3 figures. Corrected error in the calculation of J_

Open Boundaries for the Nonlinear Schrodinger Equation

We present a new algorithm, the Time Dependent Phase Space Filter (TDPSF) which is used to solve time dependent Nonlinear Schrodinger Equations (NLS). The algorithm consists of solving the NLS on a box with periodic boundary conditions (by any algorithm). Periodically in time we decompose the solution into a family of coherent states. Coherent states which are outgoing are deleted, while those which are not are kept, reducing the problem of reflected (wrapped) waves. Numerical results are given, and rigorous error estimates are described. The TDPSF is compatible with spectral methods for solving the interior problem. The TDPSF also fails gracefully, in the sense that the algorithm notifies the user when the result is incorrect. We are aware of no other method with this capability.Comment: 21 pages, 4 figure