High Throughput Virtual Screening with Data Level Parallelism in Multi-core Processors

Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements, the world might find cures for incurable diseases like HIV disease and Cancer sooner. Our approach presented in this paper is to utilize a multi-core environment to introduce Data Level Parallelism (DLP) to the Autodock Vina software, which is a widely used for molecular docking software. Autodock Vina already exploits Instruction Level Parallelism (ILP) in multi-core environments and therefore optimized for such environments. However, with the results we have obtained, it can be clearly seen that our approach has enhanced the throughput of the already optimized software by more than six times. This will dramatically reduce the time consumed for the lead identification phase in drug designing along with the shift in the processor technology from multi-core to many-core of the current era. Therefore, we believe that the contribution of this project will effectively make it possible to expand the number of small molecules docked against a drug target and improving the chances to design drugs for incurable diseases.Comment: Information and Automation for Sustainability (ICIAfS), 2012 IEEE 6th International Conference o

String Matching with Multicore CPUs: Performing Better with the Aho-Corasick Algorithm

Multiple string matching is known as locating all the occurrences of a given number of patterns in an arbitrary string. It is used in bio-computing applications where the algorithms are commonly used for retrieval of information such as sequence analysis and gene/protein identification. Extremely large amount of data in the form of strings has to be processed in such bio-computing applications. Therefore, improving the performance of multiple string matching algorithms is always desirable. Multicore architectures are capable of providing better performance by parallelizing the multiple string matching algorithms. The Aho-Corasick algorithm is the one that is commonly used in exact multiple string matching algorithms. The focus of this paper is the acceleration of Aho-Corasick algorithm through a multicore CPU based software implementation. Through our implementation and evaluation of results, we prove that our method performs better compared to the state of the art

Lady Chatterley. L'harmonie du dos retrouvée

International audienceDans son adaptation (2006) de L’amant de Lady Chatterley (D. H. Laurence), Pascale Ferran met en valeur un motif auquel le romancier, sans le négliger, n’accordait pas une place aussi importante : le dos. Cette sensibilité au motif révèle une lecture pertinente car les vues de dos rendent sensibles deux aspects déterminants du roman. D’abord, l’éveil à la sensualité. Ensuite, de façon plus souterraine, le rôle crucial qu’a joué la Renaissance dans la genèse et le souffle même de ce roman écrit en Toscane. Du dos « fragment » au début du film qui agit comme une « vision » aux dos nus des amants enlacés à la cabane, n’est-ce pas l’esprit Quattrocento qui habite cette harmonie du dos retrouvée