The collaboration for the Grid Research by Bioresearches in Osaka University and Chinese Academic of Sciences

Cybermedia Center, Osaka University
Information Network Center, Institute of Microbiology, Chinese Academy of Sciences

The collaboration for the Grid Research by Bioresearches in Osaka University and Chinese Academic of Sciences
-Biogrid Research Infrastructure Links Asian Nations

1. Overview

Cybermedia Center, Osaka University (CMC) has built an international Grid research infrastructure for bioresearches in collaboration with Information Network Center, Institute of Microbiology, Chinese Academy of Sciences (CAS). This new infrastructure is based on proprietary Grid computing technology developed by CMC. To construct the research infrastructure, we apply the Grid technology and IPv6 network technology(*1), both of which are supposed to be next-generation ITs. Moreover, we integrate CMC’s a high-performance cluster system and a CAS’s cluster system to establish an IT environment that allows users to share each othersEunique database and perform collaborative analysis on bio-related data. In addition to that, for the infrastructure being used in this collaborative research, we utilize some research results from IT program of “Construction of a Supercomputer NetworkEgranted by Ministry of Education, Culture, Science and Technology (MEXT).

2. Description

1) Research Bodies

CMC has been promoting IT program of “Construction of a Supercomputer NetworkEknown as BioGrid project under the leadership of Prof. Shinji Shimojo, Deputy Director of CMC. This five-year project is responsible mainly for the research and development for the Grid infrastructure technology targeting on bioresearches. On the other, CAS has been taking on a national project as a key player to develop Chinese domestic bio-related database. Dr. Juncai Ma, Director of CAS, is the leader of the project. China is one of megadiversity countries, where 70% of this planet's species are living. Therefore their biological resource databases contain a great deal of information on endemic species, as well as attract researchers all around the world.

2) What can be achieved through the establishment of the Grid infrastructure

In this collaborative research, the Grid infrastructure technology developed by CMC makes it possible for each researcher in both institutions to freely utilize each institution’s database. In present, such databases are CAS database treating species and biological samples of Chinese uniqueness and public database such as PDB(*2), a protein 3D structure database that the Institute for Protein Research, Osaka University operates and administers.. In near future, furthermore, CMC plans to develop the Grid research infrastructure that allows researchers and scientists to execute a variety of bio-related applications such as BLAST and CLUSTALW(*3), each of which is optimized and so is capable of reducing the analysis time of the correspondent application.

3) Technical features to develop the Grid infrastructure

This research infrastructure introduces GSI-SFS(*4) (Grid Security Infrastructure-Self-Certifying File System) and GUIDE(*5) (A Grid User Interface to the Distributed Environment) as the original technologies in BioGrid. GSI-SFS is a secure file system on the Grid. Through the use of GSI-SFS, each user can freely mount/unmount remote files systems, which can be located either at CMC or CAS. It is significant that we can safely and easily control a file of interest stored in the remote file system at user level. That is to say, each user can own a distinct disk image, meaning that GSI-SFS offers exclusiveness of disk image to users. Thus, researchers both at CAS and CMC can conduct their own research using each othersEdatabases with much security.
GUIDE is a portal system designed for the Grid system. One of the significant features in GUIDE is that it can hide complex mechanism that the Grid technology has. Even researchers who are not familiar with the Grid can freely use CMC’s Biogrid infrastructure system(*6) and CAS’s cluster system as they use GUIDE. With GUIDE, they can complete data analysis in a short period of time, even though such data analysis is very slow by conventional methods.
Pursuing the construction of the research infrastructure, CMC and CAS have already got to work on research exchange and testbeds. In the last April, CAS sent off a researcher to CMC to acquire the Grid technology. At the present stage, small-scale Grid testbeds connecting CAS and CMC is being developed. We are also actively conducting testbeds by using GSI-SFS and GUIDE.
Under this research infrastructure, computing and data resources located at CMC and CAS are shared and utilized by their researchers. We expect that development of such research infrastructure will enhance researches that Asia can promote outstandingly.
GIS-SFS, GUIDE, and technologies used for developing the Grid infrastructure are part of results performed through IT-program of MEXT.

3.R&D Bodies

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4.Future Perspectives

By next April, we will switch the current research infrastructure to IPv6 environment. Osaka University will attempt to establish a research infrastructure open to Asian countries. Currently, collaborative researches with Korea and Singapore have been initiated. If these attempts make a great success, it is expected that Asia can regain from lost ground against Europe and the US in biology.

(Glossary)
*1	IPv6 network technology
	Technology developed as the next-generation Internet protocol. Safer and higher performance network environment is made possible by the technology.

*2	PDB (Protein Data Bank)
	Protein 3D Structure Database. This database is operated by three hubs located in US, Europe and Japan. The Institute for Protein Research, Osaka University is the hub in Asia.

*3	BLAST / CLUSTALW
	Popular analysis tools for bioinformatics analysis. BLAST compares base or amino acid sequences registered into the database with sequences given by user as query. CLUSTALW is used to find out similarity from given base or amino acid sequences.

*4	GSI-SFS (Grid Security Infrastructure-Self-certifying Filesystem)
	Secure file system developed by CMC. This technology utilizes Self-certifying File system being developed by MIT, the U.S.This technology is used in the system.

*5	GUIDE ( A Grid User Interface to the Distributed Environment )
	User interface that users can use the Grid system without being aware of using it. Because the latest version of GUIDE uses for web interface, it is also considered as web portal system.

*6	Biogrid Infrastructure system
	A large-scale cluster system consisted of three clusters. The system is based on Osaka University’s NEC Blade Server and has more than 180 total processors.