Suhaimi Napis, PhD CIO and Director, InfoComm Development and Computer Centre (Interim) (iDeC2)

1. GRID Research and Applications in Malaysia: Leveraging on Malaysian Research and Education Network (MYREN) connectivity to TransEurasian Information Network and ASEAN NRENs. Suhaimi Napis, PhD CIO and Director, InfoComm Development and Computer Centre (Interim) (iDeC2) Universiti Putra Malaysia Director, E-Research Area, Malaysian Research and Education Network (MYREN) Vice Chairman, ASEAN Science and Technology Research and Education Network Alliance (ASTRENA)

2. Outline • Overview of MYREN, TEIN2, and ASTRENA • National GRID Initiative • Examples of Research Activities • Conclusion

3. TEIN2 Internet Campus Network Campus Network Campus Network Campus Network Campus Network Campus Network Campus Network Campus Network Campus Network Campus Network Campus Network Campus Network Campus Network Campus Network Mimos Grid Computing Centre MDeC Virtual Reality Cluster NAV6 Centre MONASH UNIMAS TM R&D UNITEN UTM UITM MMU UKM UUM UPM UMS USM UTP UM MYREN Network Topology (as of Aug 2006) 45M MYREN NOC 4M 4Q06 4Q06 MYREN WAN** **connects members and collaborators at national level

4. Trans-Eurasia Information Network (TEIN2) • Under TEIN 2, MYREN will connect the Asian research networks and to the Pan-European Research Network (GÉANT). Major funding from the European Commission • Help to equalise access to research networking resources • Building the bridge for ICT co-operation • Increase co-ordination in research and education • Funding for Scientific & Research projects is available through EC’s 6th and 7th Framework Programme for IST • Match-making of European and Asian scientists is through EC’s GAPFILL Programme

5. TEIN2 Topology: 45Mbps Connectivity to MYREN

6. TEIN2 Routing IPv4 block: 202.179.240.0/20IPv6 block: 2001:0254::/32 AS24489 AS24490

7. After TEIN2…

8. An ASEAN SCIRD Project

10. APAN TransPAC

11. APBioNet ASTRENA S* Alliance BioUser BioGrid SEAGridForum TEIN2-APAN

12. ASTRENA Framework Life Science Vertical Bioinformatics Physical Sciences LHC project HealthCare Remote Sensing/ Meteorol GeoInformatics Applications Services Resources Network Infrastructure

13. Proposed National GRID Initiative

14. Bird’s Eye View

15. Grid Domains

16. Proposed Bioinformatics Activities

17. Examples of Research Activities at Selected Universities

21. Research Activities at E-Science GRID Testbed • Liquid Crystal Simulation – Prof. Dr. Rauzah Ibrahim, Dept of Chemistry, UM • Molecular Docking • Dr. Habibah AbdWahab, Laboratory of Biocrystallographyand Structural Bioinformatics, USM • AutoDie from Electrical and Electronics Engineering Faculty

22. Universiti Putra Malaysia Homology Modelling Sequence alignment of T1 lipase and P1 lipase crystal structure (Clustal W) Modelled using DS Modeling 1.1 software

23. Predicted T1 lipase structure Evaluated using Ramachandran Plot, Verify 3D & Errat

24. Superimposition of crystal structure on predicted structure Red : Crystal Yellow: Predicted RMSD= 0.8

25. University of Malaya Collaborative surgery through the use of MyREN and High Performance Computing: SIDDATA(Surgery In multi-Dimensional DATA) University of Malaya

26. SGI Onyx Supercomputer Remote Client - PCs MyREN Video Conferencing 3DModel Hospital

28. Fox and Hutchins (1972). Johns Hopkins Med. J. 130(5): 289-299 Reconstructing the Heart Structure Function A common theme in biology • Myocardium is composed of fibers • Electrical current spreads fastest along the fibers • Maximum mechanical strain is along the fibers • Heart shape & fiber organization change in disease, contributing to • Pump failure • Electrical arrhythmias

29. SGI VizServer via MyRen SGI ONYX Visualization Server (CADC) SGI Tezro Visualization Server (UM-VRC) Visualization Processing Heart Application Pre-Processing Heart Application Post-processing Cluster Filesystem SAN Storage LINUX KERNEL LINUX KERNEL LINUX filesystem NFS Client NFS Server LINUX filesystem NFS Protocol via MyRen UM-VRC Master Processor CADC Storage Processor

30. Heart Model Visualization

31. Universiti Teknologi Malaysia Professor Dr Safaai Deris, Artificial Intelligence and Bioinformatics Laboratory Projects: • Learning Enhancements of Support Vector Machine for Detecting Remote Protein Homology • Predicting Protein Secondary Structure Using Artificial Neural Networks and Information Theory • Protein Secondary Structure Prediction from Amino Acid Sequences Using a Neural Network Classifier based on the Dempster-Shafer Theory • A Hybrid of Genetic Algorithm and Support Vector Machine for Genes Selection and Classification of Gene Expression Data

32. Clustering And Statistical Techniques For Gene Selection And Classification Of Gene Expression Data Automatic Clustering of Gene Ontology by Genetic Algorithm Protein Function Prediction From Protein-Protein Interaction Data Using Machine Learning Techniques Gene Network Inference Using Bayesian Network and Prior Knowledge Performance Enhancements of a Hybrid of Genetic Algorithm and Support Vector Machine for Genes Selection and Classification of Gene Expression Data A Wrapper Approach for Marker Genes Selection and Classification based on Gene Expression Data Biomarker Identification from Microarray Gene Expression Data using Genetic Algorithm for Cancer Classification

33. Summary • GRID research is active in Malaysia, mostly on bioinformatics • GRID infrastructure – only testbed; most individual research labs has their own small clusters • National GRID Initiative – Roadmapped and proposed (as I speak!) • International collaborations are on personal basis (eg. PRAGMA)

34. Conclusion • Malaysia is a latecomer in GRID and yet to be part of global GRID community on a large scale • Advantageous as best-practices has been established • Plenty of opportunities especially in lifesciences (Avian Influenza, Dengue Fever, Biodiversity profiling, etc) • Hope to be part of EGEE • Facilitation is under way to get registered and certified to start a project that has been identified

35. Special Thanks:EGEE/CERN and Taiwan GRIDfor sponsorship

36. TQ 