Large Scale In Silico Screening on Grid Infrastructures

Large-scale grid infrastructures for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale in silico docking within the framework of the WISDOM initiative against Malaria and Avian Flu requiring about 105 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large-scale grid infrastructures for the virtual screening by molecular docking. This also allowed evaluating the performances of the grid infrastructures and to identify specific issues raised by large-scale deployment.Comment: 14 pages, 2 figures, 2 tables, The Third International Life Science Grid Workshop, LSGrid 2006, Yokohama, Japan, 13-14 october 2006, to appear in the proceeding

Rational bidding using reinforcement learning: an application in automated resource allocation

The application of autonomous agents by the provisioning and usage of computational resources is an attractive research field. Various methods and technologies in the area of artificial intelligence, statistics and economics are playing together to achieve i) autonomic resource provisioning and usage of computational resources, to invent ii) competitive bidding strategies for widely used market mechanisms and to iii) incentivize consumers and providers to use such market-based systems. The contributions of the paper are threefold. First, we present a framework for supporting consumers and providers in technical and economic preference elicitation and the generation of bids. Secondly, we introduce a consumer-side reinforcement learning bidding strategy which enables rational behavior by the generation and selection of bids. Thirdly, we evaluate and compare this bidding strategy against a truth-telling bidding strategy for two kinds of market mechanisms – one centralized and one decentralized

Q-Strategy: A Bidding Strategy for Market-Based Allocation of Grid Services

The application of autonomous agents by the provisioning and usage of computational services is an attractive research field. Various methods and technologies in the area of artificial intelligence, statistics and economics are playing together to achieve i) autonomic service provisioning and usage of Grid services, to invent ii) competitive bidding strategies for widely used market mechanisms and to iii) incentivize consumers and providers to use such market-based systems. The contributions of the paper are threefold. First, we present a bidding agent framework for implementing artificial bidding agents, supporting consumers and providers in technical and economic preference elicitation as well as automated bid generation by the requesting and provisioning of Grid services. Secondly, we introduce a novel consumer-side bidding strategy, which enables a goal-oriented and strategic behavior by the generation and submission of consumer service requests and selection of provider offers. Thirdly, we evaluate and compare the Q-strategy, implemented within the presented framework, against the Truth-Telling bidding strategy in three mechanisms – a centralized CDA, a decentralized on-line machine scheduling and a FIFO-scheduling mechanisms

Virtual Screening on Large Scale Grids

PCSV, article in press in Parallel ComputingLarge scale grids for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale virtual docking within the framework of the WISDOM initiative against malaria and avian influenza requiring about 100 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large scale grids for the virtual screening by molecular docking. This also allowed evaluating the performances of the grid infrastructures and to identify specific issues raised by large scale deployment

GEANT4 : a simulation toolkit

Abstract Geant4 is a toolkit for simulating the passage of particles through matter. It includes a complete range of functionality including tracking, geometry, physics models and hits. The physics processes offered cover a comprehensive range, including electromagnetic, hadronic and optical processes, a large set of long-lived particles, materials and elements, over a wide energy range starting, in some cases, from 250 eV and extending in others to the TeV energy range. It has been designed and constructed to expose the physics models utilised, to handle complex geometries, and to enable its easy adaptation for optimal use in different sets of applications. The toolkit is the result of a worldwide collaboration of physicists and software engineers. It has been created exploiting software engineering and object-oriented technology and implemented in the C++ programming language. It has been used in applications in particle physics, nuclear physics, accelerator design, space engineering and medical physics. PACS: 07.05.Tp; 13; 2

Drilling Predation on Serpulid Polychaetes (Ditrupa arietina) from the Pliocene of the Cope Basin, Murcia Region, Southeastern Spain

We report quantitative analyses of drilling predation on the free-living, tube-dwelling serpulid polychaete Ditrupa arietina from the Cope Cabo marine succession (Pliocene, Spain). Tubes of D. arietina are abundant in the sampled units: 9 bulk samples from 5 horizons yielded ∼5925 specimens of D. arietina. Except for fragmentation, tubes were well preserved. Complete specimens ranged from 3.1 to 13.4 mm in length and displayed allometric growth patterns, with larger specimens being relatively slimmer. Drilled Ditrupa tubes were observed in all samples. Drillholes, identified as Oichnus paraboloides, were characterized by circular to elliptical outline (drillhole eccentricity increased with its diameter), parabolic vertical profile, outer diameter larger than inner diameter, penetration of one tube wall only, narrow range of drill-hole sizes, and non-random (anterior) distribution of drillholes. A total of 233 drilled specimens were identified, with drilling frequencies varying across horizons from 2.7% to 21% (3.9% for pooled data). Many tube fragments were broken across a drillhole suggesting that the reported frequencies are conservative and that biologically-facilitated (drill-hole induced) fragmentation hampers fossil preservation of complete serpulid tubes. No failed or repaired holes were observed. Multiple complete drillholes were present (3.9%). Drilled specimens were significantly smaller than undrilled specimens and tube length and drill-hole diameter were weakly correlated. The results suggest that drillholes were produced by a size-selective, site-stereotypic predatory organism of unknown affinity. The qualitative and quantitative patterns reported here are mostly consistent with previous reports on recent and fossil Ditrupa and reveal parallels with drilling patterns documented for scaphopod mollusks, a group that is ecologically and morphologically similar to Ditrupa. Consistent with previous studies, the results suggest that free-dwelling serpulid polychaetes are preyed upon by drilling predators and may provide a viable source of data on biotic interactions in the fossil record

GEANT4--a simulation toolkikt

Geant4 is a toolkit for simulating the passage of particles through matter. It includes a complete range of functionality including tracking, geometry, physics models and hits. The physics processes offered cover a comprehensive range, including electromagnetic, hadronic and optical processes, a large set of long-lived particles, materials and elements, over a wide energy range starting, in some cases, from 250 eV and extending in others to the TeV energy range. It has been designed and constructed to expose the physics models utilised, to handle complex geometries, and to enable its easy adaptation for optimal use in different sets of applications. The toolkit is the result of a worldwide collaboration of physicists and software engineers. It has been created exploiting software engineering and object-oriented technology and implemented in the C++ programming language. It has been used in applications in particle physics, nuclear physics, accelerator design, space engineering and medical physics

Comparaison de méthodes d'évaluation de la production secondaire d'une population de l'annélide polychète Ditrupa arietina (O.F. Muller)

We compared the ability of three direct methods (increment summation, loss summation and instantaneous growth rate coefficient), the size-frequency method, and eight indirect methods (Banse and Mosher, Benke, Brey, Edgar, Morin and Bourassa, Plante and Downing, Robertson and Schwinghamer et al.) to measure or to predict the secondary production of a Mediterranean population of the polychaete Ditrupa arietina. This comparison was carried out both on the 1994 cohort during its two-year lifespan and on the entire population during the two years of the study (1994-1996). Our results showed that all three direct methods are more or less equivalent. Results referring to the year 1994-1995 showed a strong overestimation of the actual production by the size frequency method. This is attributed to the existence of an average individual maximal size below which the actual production equals zero. During the same year, the results obtained using indirect methods were highly variable, partly, but not solely, due to the type of environment for which the regression models were built. The incorporation of temperature as an independent variable within the most recent regression models did not contribute to improving the quality of the predictions. Results referring to the year 1995-1996 confirm the incapacity of both the size frequency and the indirect methods to predict changes in the P/B ratio in relation with age structure and recruitment irregularities. These results are discussed in the context of inferring productivities both at the population and the community level.Nous avons comparé les aptitudes de trois méthodes directes (sommation des incréments, sommation des pertes et coefficient de croissance instantanée), de la méthode de fréquence de taille et de huit méthodes indirectes (Banse et Mosher, Benke, Brey, Edgar, Morin et Bourassa, Plante et Downing, Robertson et Schwinghamer et al.) à mesurer ou à prédire le niveau de production secondaire d'une population méditerranéenne de l'annélide polychète Ditrupa arietina. Cette comparaison a porté à la fois sur la seule cohorte ayant recruté au printemps 1994 pendant ses deux années d'existence et sur l'ensemble de la population pendant les deux années d'étude (1994–1996). Dans l'ensemble, les résultats obtenus montrent la quasi-équivalence de toutes les méthodes directes. Une forte surestimation de la production réelle par la méthode de la fréquence de taille est observée avec les résultats de l'année 1994–1995, où l'existence d'une taille moyenne maximale au-delà de laquelle la production est nulle n'est pas prise en compte. Pour cette même année, les résultats obtenus par les méthodes indirectes sont très variables avec, entre autres, le type de milieu pour lesquels les modèles ont été établis. L'introduction de la température dans les modèles les plus récents ne semble pas améliorer la qualité des prédictions. Les résultats de l'année 1995–1996 confirment l'inaptitude de la méthode de fréquence de taille et des méthodes indirectes à rendre compte de l'évolution du rapport P/B en fonction de la structure d'âge et des irrégularités du recrutement. Ces résultats sont discutés en fonction de l'utilisation possible de ces méthodes pour inférer des productivités tant à l'échelle de populations monospécifiques qu'à celle de communautés benthiques dans leur ensemble

On the dramatic increase of Ditrupa arietina O.F. Muller (Annelida: Polychaeta) along both the French and the Spanish Catalan coasts

11 páginas, 5 figuras, 2 tablas.The distribution and population structure of the serpulid polychaete Ditrupa arietina were assessed along the section of the Mediterranean coast between Barcelona and Montpellier. The study combined: (1) the analysis of the existing historical data referring to the period before the 1970s; (2) the results of impact assessment surveys carried out in the late 1980s and the 1990s; and (3) the results of two surveys carried out in the Bay of Blanes and along the coast between Cape Cerbe`re and Port-la-Nouvelle during 1996. The results of the surveys carried out in the 1990s show the occurrence of high densities (i.e. >1000 ind m"2) of Ditrupa arietina at all the sites sampled. These results can be compared with the few reports of this species before 1970, leading to the conclusion that D. arietina has recently increased all along the Catalan coast. Ditrupa arietina is preferentially found between 20 and 30 m depth, which mostly corresponds to well-sorted fine sands and muddy sands. Both the results of population monitoring and the heterogeneity of population structure at small spatial scale show that the dynamics of this species is unstable. The observed distribution pattern is therefore interpreted as resulting from a response to both wide-scale environmental parameters (accounting for the dramatic increase of the species at a wide geographical scale), and to local environmental factors (accounting for small-scale heterogeneity in population structure). Analysis of the relationship between sedimentary data and densities of D. arietina suggests that this species is highly sensitive to the presence of fine sediments. However, because of the regional importance of the phenomenon, it is concluded that the dramatic increase of D. arietina along both the Spanish and the French Catalan coast does not result from sediment instability.Some of the Spanish part of this research was funded by the CICYT MAR-91- 0503 project and by fellowships of the MEC and the CSIC to S. Pinedo and D. Martin. The authors also acknowledge the financial support of the Department de Medi Ambient of the Autonomous Community of Catalonia during the Portbou and Palamo´ s surveys.Peer reviewe