Bioinformatics Gridbased Applications and IOITHCM Grid Tran Van

Bioinformatics Grid-based Applications and IOIT-HCM Grid Tran Van Lang, Do Van Long Members of VNGrid Project HCM City Institute of Information Technology (IOIT-HCM, VAST)

IOIT-HCM Introduction Ho Chi Minh City Institute of Information Technology (IOIT-HCM, VAST)

History of IOIT-HCM Grid 2001 -2002 2003 2004 IOIT-HCM Grid Project The Centers Grid and systems Group of Conference on HPC for HPC were HCM City and Grid Computing, founded College in HCM City, held by Ministry of Science Natural and Technology Sciences 2005 Bio. Grid, IOIT-HCM BK Grid Group, Hanoi UT 2006 -2007 IOIT-HCM connect to Pragma HCM City UT Grid Project VNGrid Project

IOIT-HCM join to Pragma

PH N VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ MINH (IOIT-HCM) 5

IOIT-HCM Grid resource monitor PH N VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ MINH (IOIT-HCM) 6

PH N VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ MINH (IOIT-HCM) 7

PH N VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ MINH (IOIT-HCM) 8

Applications and Middleware in Pragma testbed http: //goc. pragma-grid. net/applications/default. html n n n Real science applications pair and drive middleware development Achieve long-run and scientific results Open to applications of all scientific disciplines Climate simulation n Savannah/Nimrod (MU, Australia) n MM 5/Mpich-Gx (CICESE, Mexico; KISTI, Korea) n Quantum-mechanics, quantum-chemistry: n TDDFT, QM-MD, FMO/Ninf-G (AIST, Japan) n Genomics n i. GAP/Gfarm/CSF (UCSD, USA; AIST, Japan; JLU, China) n HPM: genomics (IOIT-HCM, Vietnam) n mpi. Blast/Mpich-G 2 (ASGC, Taiwan) n Organic chemistry n Gamess-APBS/Nimrod (UZurich, Switzerland) n Molecular simulation n Siesta/Nimrod (UZurich, Switzerland; MU, Australia) n Amber/Rsh ( USM, Malaysia) n Computer Science n Load Balancer (IOIT-HCM, Vietnam) n Gridd. Le. S (MU, Australia) 2 applications from Vietnam 9 n

IOIT-HCM Grid Members

Infrastructure of IOIT-HCM Grid System PH N VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ MINH (IOIT-HCM) 11

Network architecture of Grid System connect to KISTI, PRAGMA and VAST PH N VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ MINH (IOIT-HCM) 12

Grid-based applications

IOIT-HCM Grid Portal n Our Grid Portal based on opensource packages: n n n n n Globus Toolkit 4 Java Co. G Jetspeed Portal Tomcat Jboss Postgresql Condor G Grid. Port 4 Grid. Sphere Framework with JSR 168 -compatible Portlet Container 14

Bio. Science n Gird Portal n n n Resource monitoring in a grid Proxy management File management Job specification and execution Building Bioinformatics tools with Grid Technology apply on Grid Portal: n n n Multiple sequences alignment Phylogenetics Tree Blast Motif finding Protein Structure Prediction

Grid Portal

Gird computing apply for generating the Phylogenetic Tree

IOIT-HCM Grid Portal - Blast deploying

Motif finding n Programming in MPI-2 apply on IOIT-HCM Grid System

Protein Structure prediction n Programming in MPI-2 with Molecular Dynamic (MD) Algorithm

Access Grid deployment n Access Grid for collaboration the multimedia data (IOIT-HCM): Support ting to the Conference on IT and Communication in Haiphong, Vietnam (10/2005)

Meeting Room 1 2 nd Floor – Block 1 Center Room 1 st Floor – Block 1 Meeting Room 3 2 nd Floor – Block 2 Meeting Room 2 1 st Floor – Block 2

Telemedicine

Telemedicine Conference on 05/05/05 Hospital of Medical (HCM) vs. Viet. Duc Hospital (Ha Noi)

Conference between Ben. Tre Province Leaders with University of Medical (HCM) Deploying Telemedicine with Access. Grid Technology from IOIT-HCM

Telemedicine between Nhi Dong 1 Hospital (HCM) and Nguyen Dinh Chieu (Ben Tre Province) Deploying Telemedicine with Video Conferencing Technology from IOIT-HCM

Setup the e-Learning system for training on Gird 2 nd Training Course on Functional Genomics of Insect Vector of Human diseases - Oct 2005, Malaria Research Center, Bamako, Africa (support from NIH, US)

Elearning system of IOIT-HCM deploy in Bamako, Mali, Afica

Bioinformatics Courses with NCBI NLM – National Library Medical Training Class NIH, US

Research for deploy Grid System in South Provinces of Vietnam Connecting from HCM to Can Tho University

Connecting from HCM to An Giang University

Avian Flu Observer research to deploy on Grid

Vietnam Digital Map research to deploy on Grid

Join to the Grid Communities 1. 2. 3. 4. 5. 6. 7. 8. 9. Geo. Grid, Pragma 12: Thailand (03/2007) ISGC 07: Taipei (03/2007) EGEE User Forum: Manchester (05/2007) Asia. Grid: Singapore (06/2007) APAN Meeting: China (08/2007) EGEE Meeting: Pudapest (10/2007) Grid Camp: Taipei (11/2007) Do Son School: Vietnam (11/2007) …

Join to the Grid Communities (cont. ) Fragma 12 – Thailand, Mar 2007 ISGC 2007 – Taipei, Apr 2007

EGEE User Forum, England , May 2007 Asia. Grid – Singapore, Jun 2007

24 th APAN Meeting- Xian, China Aug 2007 International IT Conference 10 th , Vietnam, Sep 2007

EGEE Meeting: Pudapest (10/2007) Grid Camp: Taipei (11/2007)

Future step: Setup Grid on Vina. Ren Network

Finished test TEIN 2 Connection from VNU Ha Noi to IOIT-HCM

Conclusion n n Studying Grid Technology and try to apply to Science and Education. Will invest more for the networking and infrastructure Need to connect to the other Grid System for expand the collaboration. Need more supporting to develop Our next step is connecting to EGEE Asia Federation (EAF) to receive the operations technology and experience for deploying e-Science on our Grid Resource Centers. 46