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Integrative workflows for Bio Research & Medical Research Lim Teck Sin CEO

Integrative workflows for Bio Research & Medical Research Lim Teck Sin CEO. Summary of Presentation. KOOPrime, an Introduction Workflows for Bio Research Microarray Oligo Design Sequencing Disease Surveillance Animal Management Workflows for Medical Research iTrials.

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Integrative workflows for Bio Research & Medical Research Lim Teck Sin CEO

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  1. Integrative workflows for Bio Research & Medical ResearchLim Teck Sin CEO

  2. Summary of Presentation • KOOPrime, an Introduction • Workflows for Bio Research • Microarray • Oligo Design • Sequencing • Disease Surveillance • Animal Management • Workflows for Medical Research • iTrials

  3. Mission Statement Leading Provider of IT Products and Services for the Life Sciences Industry in Asia

  4. Outreach of KOOPrime CAS HP BEIJING Mitsui Jetro JAPAN NNTP NANNING INDIA HKUST Nanshan BIOTEC SirirajH HONGKONG THAILAND MPOB MARDI NUS I2R IMCB Office/Staff MALAYSIA SINGAPORE

  5. HIGH THROUGHPUT SCREENING GENOMICS,PROTEOMICS LAB MGT AND ANALYSIS PRE-CLINICAL EVALUATION SYSTEM CLINICAL TRIAL SYSTEM FDA COMPLIANCE & VALIDATION REGISTRY& HL7 EXHANGE SYSTEM KOOP-EDUCATION SYSTEM HEALTH TRACKING SYSTEM Singapore – the Little Sparrow Bio Research Pharmaceutical KOOPLATFORM KOOPORTAL Medical Research Industrial KOOPrime’s business spans across organizations in Asia KOOPrime’s business spans across organizations in Asia

  6. BioResearch

  7. User: Malaysia Palm Oil Board User: NovusGene, Japan User: IMCB, Singapore User: National Cancer Center User: Bioprocessing Technology Center iBioSuite BioResearch Vertical Sequence Discovery Platform User: National University Singapore Oligo Discovery Platform Microarray Discovery Platform User: Malaysia Agricultural R&D Institute Animal Facility Platform Management of Genotypic Info Cut down duplication and maximize resources

  8. Microarray Discovery Platform Fabrication Barcode scanner Purification Unit Genome Mapper Clustering Pathway Gel Electrophoresis User: Bioprocessing Technology Institute User: National Cancer Center Microarray Printer Data Mining and Analysis Microarray Scanner Data Analytical Tool Data Management Genomic Data Source Proteomic Data Source Data Visualization Genome Mapper Pathway Interaction

  9. Microarray Discovery Platform KOOPServer Monitor flows KOOPBox Create/ Modify/ Execute workflows 1st Generation – RMI based KOOPlatform (1999) KOOPAgent Communicate between Different machines

  10. Microarray Discovery Platform 1st Generation – Stitching of Bubbles • Creation and deployment of bubbles • Linking ( mapping IO ) bubbles based on Workflow requirements Visual Stitching of Objects (bubbles)

  11. Microarray Discovery Platform 1st Generation – Integration Platform Create KOOP Visualize results (graphs, emails) Print results Collect machine data Broadcast results KOOPServer Download data Monitor flows Compute results

  12. Microarray Discovery Platform Microarray Fabrication Workflow (2001) Vendor File Processing PCR Plate Creation PCR Flagging Working Plate Creation Pooling Plate Creation Growth Plate Creation Pooling Growth Flagging Array Printing Plasmid Plate Creation Array QC

  13. Microarray Discovery Platform Microarray Data Management & Analysis Workflows Technical Replicate Cross Normalization Experiments Samples Biological Replicate Cross Normalization Hybridization Gene Filtering Normalization Clustering

  14. Microarray Discovery Platform Flexibility in Workflow Design via KOOPBox

  15. Microarray Discovery Platform Preparation of Probe DNAs • Probe Selection from databases ( UniGene, GenBank etc ) • Replication of 96-well-plates of bacterial clone stocks • Growth flagging of clones and restreaking of problem clones

  16. Microarray Discovery Platform Array Printing • Spotting of PCR products representing specific genes onto glass slides. • Layout 96 well plates on 384 well plates • Layout 384 well plates on DNA microarrays

  17. Microarray Discovery Platform Simplification for Non-Power Users • Maintain operator profiles based on role in a specific project • Create templates (by linking bubbles) that mimic actual workflow • Assign templates to operators Administrator’s View Operator’s View

  18. Microarray Discovery Platform Data Access Layer Presentation Layer Business Layer Servlets Session Beans Data Access Objects Internet Database Handler User JSP File System Analysis Clients 2nd Generation Web based Workflows (2002) • Go beyond Intranet • KOOPlatform 4.0: Web protocols, in addition to RMI • KOOPortal: Further simplification, accessibility to non-workflow features

  19. Microarray Discovery Platform Flexibility for Workflows

  20. Microarray Discovery Platform GLP for Microarray Fabrication Workflow

  21. Oligo Discovery Platform LivePortal Mini-PC Grid (2003) “KP's P2P technology was implemented for up-version of parallel computing environment, whichenabled heavy design calculation using internal PCs during night. This system becomes NGI's business infrastructure because of its highly cost effective performance due to almost full automated probe data base accumulation." Dr Seiichi Nemoto, General Manager, Bioinformatics Div., NovusGene Inc.

  22. Sequence Discovery Platform Ultra-Simplified Web based Workflows for 500+ Users (2004)

  23. Sequence Discovery Platform Portal to Share & Manage DNA Sequencing Resources

  24. Sequence Discovery Platform Mixed Portal-Workflow Environment (2006) Flexi analysis Routine analysis Wet Lab Sequencing Provide web based Services

  25. Sequence Discovery Platform Personalized Workflows: Phylogenetic Analysis

  26. Sequence Discovery Platform Workflows to save time: Proteomics Analysis Showorf Peptide Display CHIPS / CUSP Codon Computation fuzzpro Peptide Search Digest Cutting Positions CheckTrans ORF Output

  27. Rapid Disease Outbreak Management System To Facilitate Nation-Wide Responses to Emergencies (2005) • Measures for Disease Surveillance and Disease Outbreak management • End-to-end Integration with various Life Science ‘Lego Blocks’ • To facilitate rapid and controlled manufacturing of diagnostic kits, vaccines, etc. • To partner key organizations (e.g. IDA, MOH, NGO) to develop Outbreak IT platform Demonstration of system to minister at Asia Grid 2005

  28. Rapid Disease Outbreak Management Integration with GoalNet, Taverna, Protege

  29. Rapid Disease Outbreak Management Mapping of Resources / Bottlenecks Generate ArrayId Sample Processing Homology Search w GRIDBLAST Generate Experiment DNA Sample Plate Mapping Seq Annotation w GenBank Hybridize Array with Sample DNA Sequencing SendGeneListFile to ProbeDesign Collect Microarray Results Collect ABI data ProbeDesign Perform Single-array Normalization Store ABI data Send ProbeList to Oligo Synthesizer Filter data QualityCheck Probe QC Cross normalization Vector Masking Send CompletedProbeList to Microarray Discovery System Discovery & prediction with PCL/CS4 Vector Trimming Map ProbeToPlates Visualize with MGM or HCluster Contigs Assembly Configure Microarray Printer Generate Hits for Field test WetLab Visuals/Programs

  30. Rapid Disease Outbreak Management Detailed Mapping for Microarray Workflows Generate ArrayId Generate Experiment previous Generate Experiment Probe List Preparation Hybridize Array with Sample Clinical Sample Preparation Microarray Data Mgt Collect Microarray Results Perform Single-array Normalization Filter data Cross normalization Discovery & prediction with PCL/CS4 Microarray Discovery Microarray Visualization Visualize with MGM Primer Design Visualize with FPGA HCluster Primer/Probe Selection/Re-Design Generate Hits for Field test Hits Lits Generation Visual FPGA/NTU NYP Diagnostic Kits Manufacturing Scale up Manufacturing WetLab I2R / Taverna

  31. Animal Management Platform ‘Hotel’ system to manage workflow for 13,000 Tanks of Fishes (2006)

  32. Medical Research

  33. Medical Research Vertical User: Tan Tock Seng Hospital, Singapore User: Ministry of Health, Singapore User: National University Hospital, Singapore User: National University Hospital, Singapore iTrials Clinical Decision Support Tissue Registry HL7 Medical Data Exchange Clinical Research Platform Management of Phenotypic Information Research databanks for research and delivery

  34. iTrials - Clinical Research Platform Reports Documents Questionnaires Forms Samples Samples End-to-End Integration of Clinical Research Workflows (2006) • Data Entry • Blood Sample • Long Term Storage Clinical Centre • Recruit Interviewers • Collect Questionnaires • Blood Sample Tests • Health Screening • Urine Sample Tests • Blood Samples:

  35. iTrials - Clinical Research Platform Systematic follow-up on health screening & clinical trials

  36. iTrials - Clinical Research Platform Understand the value and cost effectiveness of clinical protocols

  37. iTrials - Clinical Research Platform Standards for Medical Records Exchange A Laboratory Message in HL7 format Message Header Segment(MSH): Intent, source, destination, syntax of message Patient Identification (PID): Patient identifying and demographic information Observation Request (OBR): A request for diagnostic services/clinical observation ZLR: Data of importance to public health, unique to lab message OBX: A single observation of individual tests performed and results

  38. Acknowledgement We Don’t Work Alone • Hewlett Packard • Bio Research sector development • HKH Bioinformatics Centre • IBM • Medical Research sector development • KOOPrime Consulting • GXP Training • Microsoft • Medical Research sector development • Nanyang Polytechnic • Pathway Genome Mapper • Nanyang Technology University • GoalNet • National University of Singapore • Domain Expertise • Disease Surveillance • Progeniq • HPC Computing Setup • FPGA Looking for partners that Specialize in Visual Components Looking for partners to Distribute iBioSuite & iTrials

  39. We Welcome Collaboration • KOOPrime SINGAPORE • 21 Science Park Road, #03-28 The Aquarius, Singapore Science Park II • Tel/Fax: 65-6775 4220/6775 4206 • KOOPrime Consulting • 21 Science Park Road, #03-28 The Aquarius, Singapore Science Park II • Tel/Fax: 65-6775 4220 X 103 /6775 4206 • KOOPrime MALAYSIA • KOOPrime (M) Sdn. Bhd., 729, Block B, Mentari Business Park, • Jalan PJS 8/5, 46150 Petaling Jaya • KOOPrime HONG KONG • HKUST-KOOPrime-HP Bioinformatics Centre, Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong • Email: KOOP-HKH@kooprime.com tecksin@kooprime.com Thank You

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