Replication and update of molecular biology databases in a grid environment

PCSV, présenté par V. Breton, à paraître dans les proceedingsUpdate of molecular biology databases is a growing burden on the biomedical research community. As the grid allows to share and replicate data, we propose a service to automatically update the biology databases from a single changing reference using web services. In this paper we report the components, the architecture and the deployment of the update service on the french RUGBI grid infrastructure. RUGBI is a computing grid infrastructure based on existing middleware and technologies for the community of scientists in bioinformatics

Large scale deployment of molecular docking application on computational grid infrastructures for combating malaria

PCSVInternational audienceComputational grids are solutions for several biological applications like virtual screening or molecular dynamics where large amounts of computing power and storage are required. The WISDOM project successfully deployed virtual screening at large scale on EGEE grid infrastructures in the summer 2005 and achieved 46 million dockings in 45 days, which is equivalent to 80 CPU years. WISDOM is one good example of a successful deployment of an embarrassingly parallel application. In this paper, we describe the improvements in our deployment. We screened ZINC database against four targets implicated in malaria. During more than 2 months and a half, we have achieved 140 million dockings, representing an average throughput of almost 80,000 dockings per hour. This was made possible by the availability of thousands of CPUs through different infrastructures worldwide. Through the acquired experience, the WISDOM production environment is evolving to enable an easy and fault-tolerant deployment of biological tool

Les grilles pour le développement médical

PCSV, présenté par V. Breton, à paraître dans les Comptes-Rendu de la ConférenceLe développement récent des sciences et technologies de l'information et de la communication permet aujourd'hui la création de véritables infrastructures pour le calcul et le stockage de données hétérogènes à l'échelle régionale, nationale et internationale. Ces infrastructures, appelées grilles informatiques, permettront bientôt d'utiliser les ressources informatiques mutualisées avec autant de facilité que nous utilisons aujourd'hui l'électricité. L'utilisation des grilles afin d'accélérer la découverte de médicaments est une voie très prometteuse pour l'avenir. Par cette approche in silico, le nombre de molécules ainsi que la vitesse de test peuvent être grandement augmentés induisant un coût moindre de développement de médicaments. Du 11 Juillet au 31 Août 2005, l'expérience WISDOM (Wide In Silico Docking On Malaria) a permis de tester rien moins qu'un million de ligands (médicaments potentiels) pour le traitement du paludisme: 1700 ordinateurs à travers le monde ont ainsi été associés à cette démarche permettant de réaliser en un mois ce qui aurait nécessité 80 ans sur un ordinateur classique. L'analyse des résultats est en cours. Par cette approche, on peut souhaiter également que les maladies orphelines puissent bénéficier d'un intérêt nouveau de la part des industries pharmaceutiques, à travers notamment la baisse du coût de développement d'un médicament, principal obstacle actuellement à leur mobilisation

The Water Vapor Abundance in Orion KL Outflows

We present the detection and modeling of more than 70 far-IR pure rotational lines of water vapor, including the 18O and 17O isotopologues, towards Orion KL. Observations were performed with the Long Wavelength Spectrometer Fabry-Perot (LWS/FP; R~6800-9700) on board the Infrared Space Observatory (ISO) between ~43 and ~197 um. The water line profiles evolve from P-Cygni type profiles (even for the H2O18 lines) to pure emission at wavelengths above ~100 um. We find that most of the water emission/absorption arises from an extended flow of gas expanding at 25+-5 kms^-1. Non-local radiative transfer models show that much of the water excitation and line profile formation is driven by the dust continuum emission. The derived beam averaged water abundance is 2-3x10^-5. The inferred gas temperature Tk=80-100 K suggests that: (i) water could have been formed in the "plateau" by gas phase neutral-neutral reactions with activation barriers if the gas was previously heated (e.g. by shocks) to >500 K and/or (ii) H2O formation in the outflow is dominated by in-situ evaporation of grain water-ice mantles and/or (iii) H2O was formed in the innermost and warmer regions (e.g. the hot core) and was swept up in ~1000 yr, the dynamical timescale of the outflow.Comment: Accepted for publication in ApJ letters [2006 August 7] (5 pages 2, figures, not edited

Detection of water at z = 0.685 towards B0218+357

We report the detection of the H_2O molecule in absorption at a redshift z = 0.68466 in front of the gravitationally lensed quasar B0218+357. We detect the fundamental transition of ortho-water at 556.93 GHz (redshifted to 330.59 GHz). The line is highly optically thick and relatively wide (15 km/s FWHM), with a profile that is similar to that of the previously detected CO(2--1) and HCO^+(2--1) optically thick absorption lines toward this quasar. From the measured level of the continuum at 330.59 GHz, which corresponds to the level expected from the power-law spectrum $S(\nu) \propto \nu^{-0.25}$ already observed at lower frequencies, we deduce that the filling factor of the H_2O absorption is large. It was already known from the high optical thickness of the CO, ^{13}CO and C^{18}O lines that the molecular clouds entirely cover one of the two lensed images of the quasar (all its continuum is absorbed); our present results indicate that the H_2O clouds are covering a comparable surface. The H_2O molecules are therefore not confined to small cores with a tiny filling factor, but are extended over parsec scales. The H_2O line has a very large optical depth, and only isotopic lines could give us the water abundance. We have also searched for the 183 GHz line in absorption, obtaining only an upper limit; this yields constraints on the excitation temperature.Comment: 4 pages, 3 figures, accepted in ApJ Letter

The Bell Laboratories (13)CO Survey: Longitude-Velocity Maps

A survey is presented of the Galactic plane in the J=1-0 transition of (13)CO. About 73,000 spectra were obtained with the 7 m telescope at Bell Laboratories over a ten-year period. The coverage of survey is (l, b) = (-5 to 117, -1 to +1), or 244 square degrees, with a grid spacing of 3' for |b| < 0.5, and a grid spacing of 6' for |b| > 0.5. The data presented here have been resampled onto a 3' grid. For 0.68 km/s channels, the rms noise level of the survey is 0.1 K on the $T_R^*$ scale. The raw data have been transformed into FITS format, and all the reduction processes, such as correcting for emission in the reference positions, baseline removal and interpolation were conducted within IRAF using the FCRAO task package and additional programs. The reduced data are presented here in the form of longitude-velocity color maps at each latitude. These data allow identification and classification of molecular clouds with masses in excess of ~ 1,000 solar masses throughout the first quadrant of the Galaxy. Spiral structure is manifested by the locations of the largest and brightest molecular clouds.Comment: 23 pages, 7 figures, ApJS submitted (out of 41 frames of Figure4, only one is included becaue of size limit