Biosciences Working Group Update

Wilfred W. Li, Ph.D., UCSD, USA

Habibah Wahab, Ph.D., USM, Malaysia

Daejeon, Korea, March 24, 2009

iDRiC Workshop

• Infectious diseases research• Epidemiological research• Cyberinfrastructure development panel

discussion• From the Biosciences WG perspective: – very effective in getting our activities known to

local researchers– further research scholar exchange opportunities

discussed

Breakout Session 1

• CNIC– Avian Flu Virtual Screening Database – Dr. Baoping Yan– Monitoring Flu Outbreaks at Qinghai Lake – Guanyuan Liu

• KISTI– Drug Screener-G – Dr. Jincheol Kim

• ASGC– Grid enabled Virtual Screening Service – Mason Hsiung

• UCSD – CADD Pipeline – Wilfred Li

• CNRS– WISDOM PE – Ana da Costa

Breakout Session 2

• Issue 1: different types of clients, different types of infrastructure/grid middleware– Drug Screener-G from KISTI, CNRS– Grid Enabled Virtual Screening Service from ASGC– CADD pipeline from UCSD

• Proposed Solution: – Biological applications are better exposed as grid

services/web services. Different clients may access services without worrying about how the jobs are distributed.

Breakout Session 2

• Issue 2: co-lead– Continuous participation of PRAGMA workshop

and Biosciences WG sessions– Leading active projects in the cyberinfrastructure

development in the Biosciences area– Familiar with international biogrid activities

• Proposed solution:– KISTI?

Breakout Session 2

• Issue 3: Avian Flu Grid datagrid GUI component– Gfarm 2.2 to be released– Opal2-CSF4 integration to be completed for TeraGrid

execution of NAMD jobs• SOAP attachment enables large input file transfer• Software as a Service poorly supported by TG

– MD trajectories remain to be managed efficiently through GUI

• Proposed solution:• Simple relational database for metadata management• Reduce the semantic layer for the time being

Other planned activities

• Further integration of Gfarm for data sharing– Gfarm v2.0 shows significant improvement in

performance and stability

• Opal-CSF4 release from sourceforge.net– This is driven by the execution of MD simulations on

different TeraGrid sites and virtual screening using the PRAGMA grid

• NBCR summer institute– Would like to have a stable CADD pipeline release for

use with the summer institute 2009

Coming activities by visiting scholars and students

• Kevin Kejun Dong is visiting Calit2/SDSC/UCSD for 6 months– Use of Dataturbine for Tile Display Wall (TDW) and CAVE – Requires development of COVISE and Dataturbine clients

• PRIME students– Up to five PRIME students may work on Avian Flu Grid related

research– USM – Malaysia; NTU – Taiwan; CNIC – China

• Possibility for new host sites for the PRIME project in 2010– Jilin University– KISTI

Thank you!

• KISTI• Daejeon – Smart City• Korea