Bioinformatics Grid-based Applications and IOIT-HCM Grid

1. 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)

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

3. 2001-2002 2003 2004 2005 IOIT-HCM Grid Project BioGrid, IOIT-HCM The Centers and systems for HPC were founded Grid Group of HCM City College Natural Sciences Conference on HPC and Grid Computing, in HCM City, held by Ministry of Science and Technology BK Grid Group, Hanoi UT HCM City UT Grid Project History of IOIT-HCM Grid 2006-2007 IOIT-HCM connect to Pragma VNGrid Project

4. IOIT-HCM join to Pragma

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

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

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

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

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

10. IOIT-HCM Grid Members

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

13. Grid-based applications

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

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

16. Grid Portal

17. Gird computing apply for generating the Phylogenetic Tree

19. IOIT-HCM Grid Portal - Blast deploying

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

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

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

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

26. Telemedicine

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

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

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

32. 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)

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

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

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

36. Connecting from HCM to An Giang University

37. Avian Flu Observer research to deploy on Grid

38. Vietnam Digital Map research to deploy on Grid

39. Join to the Grid Communities • GeoGrid, Pragma 12: Thailand (03/2007) • ISGC 07: Taipei (03/2007) • EGEE User Forum: Manchester (05/2007) • AsiaGrid: Singapore (06/2007) • APAN Meeting: China (08/2007) • EGEE Meeting: Pudapest (10/2007) • Grid Camp: Taipei (11/2007) • Do Son School: Vietnam (11/2007) • …

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

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

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

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

44. Future step: Setup Grid on VinaRenNetwork

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

46. Conclusion • 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.