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 lifestyles sciences count more and more on info te- nology to extract and deal with appropriate wisdom. The advanced computational and information administration wishes of existence technological know-how study make Grid applied sciences an enticing aid resolution. besides the fact that, many vital matters needs to be addressed sooner than the existence technology Grid turns into usual. the first overseas lifestyles technology Grid Workshop (LSGRID 2004) was once held in Kanazawa Japan, may perhaps 31–June 1, 2004. This workshop involved in lifestyles s- ence functions of grid platforms particularly for bionetwork learn and platforms 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, detailed and grid computing. Fruitful discussions came about via 18 oral shows, together with a keynote deal with and ?ve invited talks, and sixteen poster and demonstration p- sentations within the ?elds of grid infrastructure for all times sciences, platforms biology, monstrous facts processing, databases and information grids, grid portals and pipelines for practical annotation, parallel and disbursed functions, and lifestyles technology grid initiatives. The workshop emphasised the sensible points of grid techno- gies when it comes to bettering grid-enabled data/information/knowledge sharing, high-performance computing, and collaborative tasks. there has been contract one of the contributors that the development of grid applied sciences for all times technology study calls for extra concerted activities and promoting of grid purposes. We consequently concluded the workshop with the assertion of LSGRID 2005.

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Extra 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

Example text

Fig. 42 for 3000 sequences. Although it is too early to derive a concrete statement from this measurement, the result indicates that LGS cannot make use their full capacity when the number of input query sequences is less than 3000. The ratio will be worse when PC-clusters are distributed in a wide area network. 78 Giga Bytes for a query with 3000 sequences. Multistage data transfer is mandatory to deal with BLAST results. 4 Throughput Performance on Wide Area Network The GRIDBLAST throughput performance strongly depends on communication overhead in wide area networks.

The TITech GRIDBLAST site consists of six NCBI BLAST systems running on six single-CPU personal computers scheduled by CONDOR[7]. The NEC GIRDBLAST site consists of twelve NCBI BLAST systems running on a 12-cpu PC cluster scheduled by SCORE/PBS. 37 Giga Bytes BLAST results for the BLAST parameters in table 2. 5 Conclusion We have designed and developed a prototype of a high throughput GRIDBLAST services (OBIGbs) on Open Bioinformatics Grid (OBIGRID). The GRIDBLAST system gives network transparent BLAST services by encapsulating architectural differences while pursuing maximum performance of local computer resources by tuning BLAST implementations and job schedulers suitable to computer architectures on each site.

All nodes have a copy or some portion of a database. Any node in this model can split a query into sub-queries and asks other nodes to execute the sub-queries. A database is stored in each node in advance. The database can be deployed on demand but a complicated database management mechanism is required to keep data consistency. Task management becomes simpler if a resource manager is provided as a hybrid peer-to-peer model. A cooperative model is a mixture of a master-slave model and a peer-to-peer model.

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