Bioinformatics Grid-based Applications and IOIT-HCM Grid

Bioinformatics Grid-based Bioinformatics Grid-based Applications and IOIT-HCM GridApplications and IOIT-HCM Grid

Tran Van Lang, Do Van LongTran Van Lang, Do Van LongMembers of VNGrid ProjectMembers of VNGrid Project

HCM City Institute of Information HCM City Institute of Information Technology (IOIT-HCM, VAST)Technology (IOIT-HCM, VAST)

IOIT-HCM IntroductionIOIT-HCM Introduction

Ho Chi Minh City Institute of Ho Chi Minh City Institute of Information Technology Information Technology

(IOIT-HCM, VAST)(IOIT-HCM, VAST)

History of IOIT-HCM GridHistory of IOIT-HCM Grid

2003 2004 20052001-2002

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

2006-2007

IOIT-HCM connect to

Pragma

VNGrid Project

IOIT-HCM join to PragmaIOIT-HCM join to Pragma

PHÂN VIỆN CÔNG NGHỆ PHÂN VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ THÔNG TIN TẠI TP. HỒ CHÍ

MINH (IOIT-HCM)MINH (IOIT-HCM) 55



IOIT-HCM Grid resource IOIT-HCM Grid resource monitormonitor





99

Applications and Middleware Applications and Middleware in Pragma testbedin Pragma testbed

http://goc.pragma-grid.net/applications/default.html

Real science applications pair and drive Real science applications pair and drive middleware developmentmiddleware development

Achieve long-run and scientific resultsAchieve long-run and scientific results Open to applications of all scientific disciplinesOpen to applications of all scientific disciplines

Climate simulationClimate simulation Savannah/Nimrod (MU, Australia)Savannah/Nimrod (MU, Australia) MM5/Mpich-Gx (CICESE, Mexico; KISTI, MM5/Mpich-Gx (CICESE, Mexico; KISTI,

Korea)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) GenomicsGenomics

iGAP/Gfarm/CSF (UCSD, USA; AIST, Japan; iGAP/Gfarm/CSF (UCSD, USA; AIST, Japan; JLU, China)JLU, China)

HPM: genomics (IOIT-HCM, Vietnam)HPM: genomics (IOIT-HCM, Vietnam) mpiBlast/Mpich-G2 (ASGC, Taiwan)mpiBlast/Mpich-G2 (ASGC, Taiwan)

Organic chemistryOrganic chemistry Gamess-APBS/Nimrod (UZurich, Gamess-APBS/Nimrod (UZurich,

Switzerland)Switzerland) Molecular simulationMolecular simulation

Siesta/Nimrod (UZurich, Switzerland; MU, Siesta/Nimrod (UZurich, Switzerland; MU, Australia)Australia)

Amber/Rsh ( USM, Malaysia)Amber/Rsh ( USM, Malaysia) Computer ScienceComputer Science

Load Balancer (IOIT-HCM, Vietnam)Load Balancer (IOIT-HCM, Vietnam) GriddLeS (MU, Australia)GriddLeS (MU, Australia)

2 applications from Vietnam2 applications from Vietnam

http://goc.pragma-grid.net/applications/default.html

IOIT-HCM Grid MembersIOIT-HCM Grid Members



Infrastructure of IOIT-HCM Grid SystemInfrastructure of IOIT-HCM Grid System

Ethernet – 1 GbpsEthernet –10 Mbps

Ethernet 1 Gbps

Internet

172.25.100.2 172.25.100.3 172.25.100.5

172.25.100.1

172.25.101.2 172.25.101.3

172.25.101.1

172.25.97.28203.162.99.117

172.25.97.30203.162.99.98

172.25.98.118203.162.99.118

172.25.97.10203.162.99.116

biogrid.ioit-hcm.ac.vn bio.ioit-hcm.ac.vn

moon.ioit-hcm.ac.vn

Head Node (Condor)

Head Node(Condor)

Grid Portal Database

Compute Node Compute Node

CA

Ethernet – 100 Mbps

Head NodeCA (SGE)

172.25.97.29

Compute Node

172.25.102.2 172.25.102.3

172.25.102.4

172.25.102.5

172.25.102.1

venus.ioit-hcm.ac.vn

IOIT-HCM LAN



Network architecture of Grid System Network architecture of Grid System connect to KISTI, PRAGMA and VASTconnect to KISTI, PRAGMA and VAST

Internet

Compute Nodes

Ethernet

PBS

Ethernet

SGE

proliant.vast-hcm.ac.vn

198.202.88.52

150.183.249.14

rocks-52.sdsc.edu

Compute Nodes

Ethernet

Ethernet

jupiter.gridcenter.or.kr

210.86.238.85

SGE

IOIT-HCM Grid

Grid-based applicationsGrid-based applications

1414

IOIT-HCM Grid PortalIOIT-HCM Grid Portal

Our Grid Portal based on Our Grid Portal based on opensource packages:opensource packages: Globus Toolkit 4 Globus Toolkit 4 Java CoGJava CoG Jetspeed PortalJetspeed Portal Tomcat Tomcat Jboss Jboss PostgresqlPostgresql Condor GCondor G GridPort4GridPort4 GridSphere Framework with GridSphere Framework with

JSR168-compatible Portlet JSR168-compatible Portlet ContainerContainer

BioScienceBioScience Gird Portal Gird Portal

Resource monitoring in a gridResource monitoring in a grid Proxy managementProxy management File managementFile management Job specification and execution Job specification and execution

Building Bioinformatics tools with Grid Technology Building Bioinformatics tools with Grid Technology apply on Grid Portal: apply on Grid Portal: Multiple sequences alignmentMultiple sequences alignment Phylogenetics TreePhylogenetics Tree BlastBlast Motif findingMotif finding Protein Structure PredictionProtein Structure Prediction

Grid PortalGrid Portal

Gird computing apply for generating the Phylogenetic Tree

1

2

3

4

5

3

2

Align a sequence to a profile

Align a profile to a profile

Align a sequence to a sequence

11

2

3

4

5

3

2

Align a sequence to a profile

Align a profile to a profile

Align a sequence to a sequence

1

IOIT-HCM Grid Portal - Blast deploying

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

tem

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

Algorithm

http://gridportal.ioit-hcm.ac.vn:8080/gridsphere/

http://gridportal.ioit-hcm.ac.vn:8080/gridsphere/

Access Grid deploymentAccess Grid deployment

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

Meeting Room 1 2nd Floor – Block 1

Meeting Room 32nd Floor – Block 2

Meeting Room 21st Floor – Block 2

Center Room1st Floor – Block 1

TelemedicineTelemedicine

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

Noi)Noi)

Conference between BenTre Province Leaders with University of Medical (HCM)Conference between BenTre Province Leaders with University of Medical (HCM)Deploying Telemedicine with AccessGrid Technology from IOIT-HCMDeploying Telemedicine with AccessGrid Technology from IOIT-HCM

Telemedicine between Nhi Dong 1 Hospital (HCM) Telemedicine between Nhi Dong 1 Hospital (HCM) and Nguyen Dinh Chieu (Ben Tre Province)and Nguyen Dinh Chieu (Ben Tre Province)

Deploying Telemedicine with Video Conferencing Technology from IOIT-HCMDeploying Telemedicine with Video Conferencing Technology from IOIT-HCM

Setup the e-Learning system for Setup the e-Learning system for training on Girdtraining 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, AficaElearning system of IOIT-HCM deploy in Bamako, Mali, Afica

Bioinformatics Courses with NCBI

NLM – National Library Medical Training ClassNIH, US

Research for deploy Grid System in Research for deploy Grid System in South Provinces of VietnamSouth Provinces of Vietnam

Connecting from HCM to Can Tho University

Connecting from HCM to An Giang University

Avian Flu Observer research to deploy on Avian Flu Observer research to deploy on GridGrid

Vietnam Digital Map research to deploy on Vietnam Digital Map research to deploy on GridGrid

Join to the Grid CommunitiesJoin to the Grid Communities

1.1. GeoGrid, Pragma 12: GeoGrid, Pragma 12: ThailandThailand (03/2007) (03/2007)

2.2. ISGC 07: ISGC 07: TaipeiTaipei (03/2007) (03/2007)

3.3. EGEE User Forum: EGEE User Forum: ManchesterManchester (05/2007) (05/2007)

4.4. AsiaGrid: AsiaGrid: SingaporeSingapore (06/2007) (06/2007)

5.5. APAN Meeting: APAN Meeting: ChinaChina (08/2007) (08/2007)

6.6. EGEE Meeting: EGEE Meeting: PudapestPudapest (10/2007) (10/2007)

7.7. Grid Camp: Grid Camp: TaipeiTaipei (11/2007) (11/2007)

8.8. Do Son School: Do Son School: VietnamVietnam (11/2007) (11/2007)

9.9. ……

Join to the Grid Communities (cont.)Join to the Grid Communities (cont.)

Fragma 12 – Thailand, Mar 2007

ISGC 2007 – Taipei, Apr 2007

EGEE User Forum, England ,EGEE User Forum, England ,

May 2007May 2007AsiaGrid – Singapore, AsiaGrid – Singapore,

Jun 2007Jun 2007

International IT Conference 10th ,Vietnam, Sep 200724th APAN Meeting- Xian, China

Aug 2007

EGEE Meeting: EGEE Meeting: PudapestPudapest (10/2007)(10/2007) Grid Camp: Grid Camp: TaipeiTaipei (11/2007) (11/2007)

Future step: Setup Grid on VinaRen Future step: Setup Grid on VinaRen NetworkNetwork

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

4646

ConclusionConclusion Studying Grid Technology and try to Studying Grid Technology and try to

apply to Science and Education. apply to Science and Education. Will invest more for the networking and Will invest more for the networking and

infrastructure infrastructure Need to connect to the other Grid Need to connect to the other Grid

System for expand the collaboration.System for expand the collaboration. Need more supporting to developNeed more supporting to develop

Our next step is connecting to EGEE Asia Federation (EAF) Our next step is connecting to EGEE Asia Federation (EAF) to receive the operations technology and experience for to receive the operations technology and experience for deploying e-Science on our Grid Resource Centers.deploying e-Science on our Grid Resource Centers.

Documents

Bioinformatics Grid-based Applications and IOIT-HCM Grid