Grid Computing in Life Science: First International Workshop by Hideaki Sugawara (auth.), Akihiko Konagaya, Kenji Satou

By Hideaki Sugawara (auth.), Akihiko Konagaya, Kenji Satou (eds.)

Researchers within the ?eld of existence sciences depend more and more on details te- nology to extract and deal with appropriate wisdom. The advanced computational and information administration wishes of lifestyles technology study make Grid applied sciences an enticing aid answer. even if, many very important concerns has to be addressed sooner than the existence technology Grid turns into standard. the first overseas existence technology Grid Workshop (LSGRID 2004) was once held in Kanazawa Japan, may well 31–June 1, 2004. This workshop interested by existence s- ence functions of grid platforms specifically for bionetwork examine and structures biology which require heterogeneous facts integration from genome to phenome, mathematical modeling and simulation from molecular to inhabitants degrees, and high-performance computing together with parallel processing, designated and grid computing. Fruitful discussions happened via 18 oral shows, together with a keynote tackle and ?ve invited talks, and sixteen poster and demonstration p- sentations within the ?elds of grid infrastructure for all times sciences, structures biology, substantial information processing, databases and information grids, grid portals and pipelines for practical annotation, parallel and dispensed functions, and existence technological know-how grid tasks. The workshop emphasised the sensible points of grid techno- gies by way of enhancing grid-enabled data/information/knowledge sharing, high-performance computing, and collaborative initiatives. there has been contract one of the individuals that the development of grid applied sciences for all times technology study calls for extra concerted activities and promoting of grid functions. We as a result concluded the workshop with the declaration of LSGRID 2005.

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Additional info for Grid Computing in Life Science: First International Workshop on Life Science Grid, LSGRID 2004, Kanazawa, Japan, May 31-June 1, 2004, Revised Selected and Invited Papers

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Simple examples of command lines, an EMS, and an ESS are presented in Fig. 4, Fig. 5, and Fig. 6, respectively. Below we explain a typical flow of procedures in an EMS. Items (2) to (4) correspond to the bold comment lines in the script of Fig. 5. (1) Set System Parameters At least 2 system parameters, the computing environment and the concurrency, should be set when running ESM. The computing parameter specifies what type of facilities the ESM should use to run and control the jobs. The concurrency parameter specifies the maximum number of CPUs that the system can use simultaneously.

5 Result Formatter (RF) The RF unit reforms BLAST results into a format specified by a user. It is guaranteed to return a BLAST result in the format of a conventional sequential BLAST returns. The above five functional units enable us to built GRIDBLAST services (OBIGbs) for large scale BLAST queries on distributed computers connected by a VPN on the Internet. OBIGbs also prepares a web interface as a front end of BLAST search. A user can receive a URL of BLAST search result by e-mail. The system architecture is so flexible that it can make use of various kinds of computer architectures, BLAST implementations and job schedulers.

They enable us to develop a cooperative GRIDBLAST system between a server and heterogeneous remote worker nodes: which consist of various computer architectures, different BLAST implementations and different Job schedulers operated by local resource management policy. 37 Giga byte result file. ) requires intensive homology search to known genomic sequences because genomic information is a basis of the central dogma in molecular biology. The increase of genomic information requires masses of computational power for high-throughput homology services to deal with thousands of query sequences at one time.

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