PRAGMA Working Groups

Biological Sciences

The Bioscience Working Group has established several projects that are of interest to participating members. The goal? To reach a common goal of conducting routine scientific investigations using the evolving grid infrastructure, while developing the necessary missing components in collaboration with other working groups, and disseminating the lessons learned.

Seven different institutes contributed to the CCGrid 2006 publication on the deployment of scientific applications on the grid.The lessons learned came from using Nimrod/G, Gfarm, MPICH-G2, and Ninf-G on applications ranging from quantum chemistry to computational biology and bioinformatics.

Members of the Bioscience Working Group actively participated in the PRIME and PRIUS projects, and the interactions among the programs’ students and mentors have developed several important research and software development programs. Over the summer, PRIME researchers from UCSD at China’s CNIC did research on virtual screening of new inhibitors for avian flu surface proteins. Another part of the project involves the initial planning for an avian flu database. UCSD and Osaka PRIUS teams extended the Opal web service toolkit to the Web Service Resource Framework (WSRF) as Opal operation provider.

Additional interactions among PRIUS host sites (University of Queensland and UCSD) through PRIUS students, and among summer interns from Jilin University at UCSD, contributed to the development of the PRAGMA Bioscience portal, with applications such as MEME and NAMD available as portlets. Additional applications will come from contributions from other participating members as GridSphere portlets. The Jilin University team developed a visual interface to CSF4 using GridSphere portlet technology. As part of the ongoing experiment using Gfarm, UCSD, JLU and Tsukuba University teams deployed native bioinformatics applications such as MEME and continue to improve the performance and scalability of the Gfarm/CSF4 environment for biological applications. The metagenomics annotation effort will begin to drive future development efforts of the Bioscience Working Group.

BIOSCIENCE: K. Jeong, Konkuk Univ., Chair; A. Krishnan, F. Tang, A. Shahab, BII Singapore; S.T. Hwang, Kookmin Univ.; J. Lee, K. Kee, K. Cho, KISTI; W. Li, SDSC at UCSD, K. Baldridge, SDSC and Univ. Zurich, P. Arzberger, UCSD; S. Hatano, Y. Qin, E. Zhang, Z. Lu, Chinese Acad. of Sci; S. Shimojo, S. Date, S. Takeda, Osaka Univ.; X. Wei, Jilin Univ.; H. Lee, ASCC; collaborabor E. McMahon, U Wisconsin.

Telescience

The Telescience Working Group aims to create and develop new information technology that allows scientists to remotely use advanced, scientific devices and to show a form of future science on an advanced cyberinfrastructure. Examples of such devices include high-accuracy scientific measurement devices such as ultra-highvoltage electron microscopes and synchrotron facilities, and highly sophisticated visualization facilities such as tiled display walls. The working group’s activities have gained in importance and expanded year by year because of the ubiquity and maturity of high-speed network technology.

The R&D activities in the Telescience Working Group fall into two types of projects. The first–and traditional–activity is the establishment of a grid workbench for neuroscience, which would allow experts to use electron microscopes and control them remotely. The second is Ecology Grid which originated in Taiwan.

TELESCIENCE: F. Lin and S. Shimojo; Co-chairs; S. Kato, T. Akiyama, K. Nozaki, Osaka Univ.; M. Lee, KISTI; D. McMullen, Indiana Univ.; K. Mikami, Cray Inc.; B. Durnota, Complexibotics; M. Ellisman, S. Peltier, A. Lin, D. Lee, T. Molina, NCMIR at UCSD; I. Kim, KBSI; H. Chou, S-I Lin, S. Cheng, NCHC; S. Ninomiya, NARC and APAN; B. Pailthorpe, N. Bordes, U Queensland; T. Fountain, S. Tilak, UCSD; H. King, Taiwan Forest Research Inst; T. Kratz, N. Temperate Lakes LTER; D. Hamilton, U Waikato.

Resources and Data

The Resources and Data Working Group’s goal is to improve the interoperability of grid middleware around the world and to make grids easier to use for scientists. During the past year, the group has expanded PRAGMA’s Grid testbed and routine-basis experiments, taking the lead in establishing Grid Interational Now (GIN) application testbed and in conducting GIN experiments in the GIN application testbed. Furthermore, the Data Computing Working Group has been combined with the Resources Working Group, to begin to build a data-grid as part of the routine-basis testbed.

The PRAGMA testbed grew from 19 sites in 13 countries to 26 sites in 14 countries, with a total of 726 CPUs, more than half a terabyte of memory, and 13.2 terabytes of online storage. For more details see the Grid Operation Center (GOC).

RESOURCES AND DATA: M. Katz, Co-chair, SDSC at UCSD; Y Tanaka, Chair, AIST; Y. Tanimura, H. Takemiya, T. Ikegami, AIST; H. Shih, eric Yen, ASGC; L.W. Kit, S. Wong, BII Singapore; O. Tatebe, CCS; S. Castaneda, J. Delgado, R. Hazas, CICESE; K. Dong, K. Nan, CNIC; S. Chen, H. Zhang, Y.L. Shi, GUCAS; Z.H. Ding, X. Wei, JLU; H.V. Nguyen; V.D. Kieu; T.V. Lang, M. Trang, T. Du, IOT-HCM; D. Ta, H.M. Chan, IHPC; S. Kim, P. Lee, KISTI; S. Sriprayoonsakul, S. Phatanapherom, P. Uthayopas, KU; J.Y. Luke, W. Hassan, MIMOS; C. Endicott, D. Abramson, MU; C.L. Huang, W. Huang, NCHC; T. Roney, R. Nandkumar, NCSA; S. Prueksaaroon, S. Vannarat, NECTEC; N. Teow, H.Y. Lee, NGO; F. Lee, J.W. Lee, NTU Singapore; S. Takeda, S. Date, Osaka U; A. Wright, R. Chhabra, QUT; C. Zheng, P. Papadopoulos, SDSC at UCSD; T. Chiba, S. Matsuoka, TITECH; A. Garcia, UBC; J.C. Maureira, A. Jofre, Univ. Chile; H. Zhang, M. Liu, UMC; E. Murrieta Leon, J.L. Gordilla Ruiz, UNAM; R. Wankar, N. Reddy, A. Agarwal, UoHyd; B. Yaik, F. Haron, C.H. Yong, Suhaini Ahmad, Habibah Wahab; USM, K. Baldridge, UniZH and SDSC; C. Amoreira, M. Packard, UniZH; X. Fan, T.N. Truong, U. Utah.