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

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Presentation transcript:

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 Conference on HPC and Grid Computing, in HCM City, held by Ministry of Science and Technology The Centers and systems for HPC were founded IOIT-HCM Grid Project HCM City UT Grid Project BK Grid Group, Hanoi UT Grid Group of HCM City College Natural Sciences BioGrid, IOIT-HCM IOIT-HCM connect to Pragma VNGrid Project

IOIT-HCM join to Pragma

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

6 IOIT-HCM Grid resource monitor

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

8

9 Applications and Middleware in Pragma testbed Real science applications pair and drive middleware development Real science applications pair and drive middleware development Achieve long-run and scientific results Achieve long-run and scientific results Open to applications of all scientific disciplines Open to applications of all scientific disciplines Climate simulation Climate simulation Savannah/Nimrod (MU, Australia) Savannah/Nimrod (MU, Australia) MM5/Mpich-Gx (CICESE, Mexico; KISTI, Korea) MM5/Mpich-Gx (CICESE, Mexico; KISTI, Korea) Quantum-mechanics, quantum-chemistry: Quantum-mechanics, quantum-chemistry: TDDFT, QM-MD, FMO/Ninf-G (AIST, Japan) TDDFT, QM-MD, FMO/Ninf-G (AIST, Japan) Genomics Genomics iGAP/Gfarm/CSF (UCSD, USA; AIST, Japan; JLU, China) iGAP/Gfarm/CSF (UCSD, USA; AIST, Japan; JLU, China) HPM: genomics (IOIT-HCM, Vietnam) HPM: genomics (IOIT-HCM, Vietnam) mpiBlast/Mpich-G2 (ASGC, Taiwan) mpiBlast/Mpich-G2 (ASGC, Taiwan) Organic chemistry Organic chemistry Gamess-APBS/Nimrod (UZurich, Switzerland) Gamess-APBS/Nimrod (UZurich, Switzerland) Molecular simulation Molecular simulation Siesta/Nimrod (UZurich, Switzerland; MU, Australia) Siesta/Nimrod (UZurich, Switzerland; MU, Australia) Amber/Rsh ( USM, Malaysia) Amber/Rsh ( USM, Malaysia) Computer Science Computer Science Load Balancer (IOIT-HCM, Vietnam) Load Balancer (IOIT-HCM, Vietnam) GriddLeS (MU, Australia) GriddLeS (MU, Australia) 2 applications from Vietnam

IOIT-HCM Grid Members

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

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

Grid-based applications

14 IOIT-HCM Grid Portal Our Grid Portal based on opensource packages: Our Grid Portal based on opensource packages: Globus Toolkit 4 Globus Toolkit 4 Java CoG Java CoG Jetspeed Portal Jetspeed Portal Tomcat Tomcat Jboss Jboss Postgresql Postgresql Condor G Condor G GridPort4 GridPort4 GridSphere Framework with JSR168-compatible Portlet Container GridSphere Framework with JSR168-compatible Portlet Container

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

Grid Portal

Gird computing apply for generating the Phylogenetic Tree

IOIT-HCM Grid Portal - Blast deploying

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

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

Access Grid deployment Access Grid for collaboration the multimedia data (IOIT-HCM): 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 Meeting Room 3 2 nd Floor – Block 2 Meeting Room 2 1 st Floor – Block 2 Center Room 1 st Floor – Block 1

Telemedicine

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

Conference between BenTre Province Leaders with University of Medical (HCM) Deploying Telemedicine with AccessGrid 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 2nd 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. GeoGrid, Pragma 12: Thailand (03/2007) 2. ISGC 07: Taipei (03/2007) 3. EGEE User Forum: Manchester (05/2007) 4. AsiaGrid: Singapore (06/2007) 5. APAN Meeting: China (08/2007) 6. EGEE Meeting: Pudapest (10/2007) 7. Grid Camp: Taipei (11/2007) 8. Do Son School: Vietnam (11/2007) 9. …

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

EGEE User Forum, England, May 2007 AsiaGrid – Singapore, Jun 2007

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

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

Future step: Setup Grid on VinaRen Network

Finished test TEIN2 Connection from VNU Ha Noi to IOIT-HCM

46 Conclusion Studying Grid Technology and try to apply to Science and Education. Studying Grid Technology and try to apply to Science and Education. Will invest more for the networking and infrastructure Will invest more for the networking and infrastructure Need to connect to the other Grid System for expand the collaboration. Need to connect to the other Grid System for expand the collaboration. Need more supporting to develop 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. 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.