biosciences working group update wilfred w. li, ph.d., ucsd, usa habibah wahab, ph.d., usm, malaysia...

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