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Oracle Life Sciences Platform and 10 g Preview

Session id: 40263 . Oracle Life Sciences Platform and 10 g Preview. Charlie Berger Sr. Director of Product Management, Life Sciences and Data Mining charlie.berger@oracle.com Oracle Corporation.

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Oracle Life Sciences Platform and 10 g Preview

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  1. Session id: 40263 Oracle Life Sciences Platform and 10g Preview Charlie BergerSr. Director of Product Management, Life Sciences and Data Mining charlie.berger@oracle.com Oracle Corporation

  2. Welcome to the Oracle Life Sciences User Group MeetingOracle HQBldg 350 Conference CenterRedwood Shores, CASeptember 10th, 20038:30 am-7:30 pm

  3. Oracle Life Sciences Day & User Group Meeting Agenda 8:00-8:30 Breakfast 8:30-8:45 Welcome 8:45-9:45 Oracle's Platform for Life Sciences - New 10G Features Preview & Solicitation Process for Features in Next ReleaseCharlie Berger, Oracle Corporation 9:45-10:30 New In Silico Drug Discovery Integrated DemoJoyce Peng, Oracle Corporation 10:30-10:50 Break 10:50-11:30 European Bioinformatics Institutes (EBI), Peter Stoehr Managing Scientific Literature (Medline) and XML Data Within Oracle 11:30-12:10 The Wellcome Trust Sanger Institute, Martin WidlakeImplementing a Terascale Data Store (20 TB) 12:10-1:00 Lunch & Wish List Feature Post-it Notes 1:00-1:40 Wyeth Research, Peter Smith21 CFR PART 11 via Oracle Auditing at Wyeth

  4. Oracle Life Sciences Day & User Group Meeting Agenda 1:40-2:20 Sequence Search Capabilities in the Database, Myriad Proteomics 2:20-3:00 Johnson & Johnson, Richard Guida & Rajesh ShahBuilding a Secure Infrastructure with Oracle in Life Sciences, J & J PKI and Secure Connectivity to Oracle 3:00-3:20 Break & Afternoon Refreshments 3:20-4:00 Kyoto University, Japan, Susumu GotoIntegrating Biological Information and Pathways using Oracle,KEGG at Kyoto University 4:00-4:40 BioMed Central Limited, Matthew CockerillManaging Scientific Images with Oracle - Multimedia Database Improves the Bottom Line 4:40-5:20 Abbott Laboratories, Shon NaeymiradElectronic Records, 21 CFR Part 11 and Oracle 9i 5:20-5:30 Break 5:30-6:30 ISV Lightening Rounds, Life Sciences ISV Partners 6:30-7:30 ISV Reception and Demo Grounds

  5. Oracle’s Commitment • "My industry is going to become pretty boring soon – • I don't believe you'll ever see this proliferation of informatics • companies or computer companies like you saw • in the decade of the Nineties. The life sciences industry • is where the horizons are wide open. There'll be lots and lots • of companies born, lots of new products, lots of new science • at least for the next 50 years. • Because of that...we've decided to focus heavily • on the life sciences industry.” • Larry Ellison, CEO, Oracle Corporation, • Bio-IT World magazine, premier issue March 2002

  6. Life Sciences Value Chain Discovery Public/Private Data In Silico Development SampleData Pharmaceutical Company Wet Lab Pharmaceutical Company Pre-Clinical Trials Biotech /PharmaceuticalResearch Labs Pharmaceutical Mfg. Plant Clinical Trials BiomedicalFirm RegulatoryAgency BiomedicalFirm Contract Research Organization Distribution Pharmacy Manufacturing, Salesand Marketing Hospital

  7. Oracle’s Solutions for Life Sciences Discovery Manage all your data Run all your applications Discovery Development & Clinical Finance HR Projects Maintenance Sales & Marketing Manufacture/ Supply Chain Management Database ApplicationServer

  8. Competition from Generics Goal: Accelerate the Discovery Process R & D Costs R & D Costs Product Launch Identify and Validate Targets Identify and Validate Leads Pre- Clinical Trails Clinical Trials Drug Discovery Economics 101Better Data Management Accelerates Discovery Revenue Sales Revenue 15 20 Years Patent Expiry Costs Identify and Validate Targets Identify and Validate Leads Pre- Clinical Trails Clinical Trials Source: Ernst & Young, Price Waterhouse

  9. Life Sciences DiscoveryGenes and Proteins Run the Cell Organism Nucleus Cell Chromosome Gene (DNA) Protein Gene (mRNA) Graphics courtesy of the National Human Genome Research Institute

  10. Life Sciences ChallengeCorrelate Biological and DNA Variation 3.2 billion letters of human DNA ~ 2 million variation points (SNPs) SNP = Single Nucleotide Polymorphism agaatttcat at[T/C]gtg gaagaggac Graphics courtesy of the National Human Genome Research Institute

  11. Life Sciences ChallengeCorrelate Diseases, Genes and Environment Schizophrenia Stroke Manic-depression Breast cancer Myocardial Infarction Diabetes Hypertension Obesity Hyperlipidemia Inflammatory Bowel Disease Graphics courtesy of the National Human Genome Research Institute

  12. Life Science Challenge Exploding Volumes of Data 500TB “To meet the scientific goals we believe we need to add around 80 - 100TB of storage each year for the next 5 years”P. Butcher, The Sanger Centre 450TB 400TB 350TB 300TB 250TB Data StorageToday 200TB 150TB 100TB 50TB 0 1994 1995 1996 1997 1998 2002 2003 2004 2005 2006 Jan-01 Oct-1999 Apr-2000 Nov-2001

  13. Life Science Challenge Many Different Kinds of Data Genomics Proteomics Modeling Pathways Clinical Pharmaco- genomics Functional Genomics Chem-informatics Graphic modified from original courtesy of Sun Microsystems

  14. Life Science Challenge Just A Few Biological Databases

  15. Manage vast quantities of data Accessheterogeneous data Collaborate securely Integrate a variety of data types Access heterogeneous Data Find Patterns and insights Life Science ChallengeTypical Research Environment Public Databases Local Databases Industrial Research Lab Local Copies Partner or Collaborator Private/Service Databases

  16. Oracle Vision :At the core is a data management platform Run All Your Applications Manage All Your Data Browser Mobile Device Oracle10g Database Server Clients Oracle10g App Server

  17. Introducing Oracle 10g • Runs all your applications • Stores all your information • Highly scalable, available, reliable • Secure • Easy to manage • Make individual systems self-managing • Manage thousands of servers at once

  18. Oracle’s Platform for Life Sciences Genomics Proteomics Cheminformatics Pathways Clinical • Access heterogeneous data • Integrate a variety of data types • Manage vast quantities of data • Find patterns and insights • Collaborate securely

  19. Manage vast quantities of data Accessheterogeneous data Access heterogeneous Data Oracle Life Sciences Platform Collaborate securely Integrate a variety of data types Find Patterns and insights

  20. Manage vast quantities of data Accessheterogeneous data Access heterogeneous Data Oracle Life Sciences Platform Transparent Gateways Fast access using Oracle OCI Distributed Queries Perform searches across domains Generic Gateways Access any data using ODBC Collaborate securely e.g. MySQL GenBank e.g. PubMed External Tables Ability to index and query external files UltraSearch Search external sites & repositories MySQL Toolkit Easily move MySQL data into Oracle Real Application Clusters Linear scalability Oracle Portal Build personalized portals Application Server Provide scalability for themiddle tier XML DB Flexibly manage data interMedia Store & manage images Security Enforce security Auditing Create audit trail to facilitate FDA compliance Workflow Automate laboratory & business processes Collaboration Suite Collaborate securely iFS/Files Share documents Integrate a variety of data types Find Patterns and insights e.g. SwissProt SP-ML Extensibility Framework (Data cartridges), manage complex scientific dataLOBs Manage unstructured data Text Index & query text, e.g. literature searches Data Mining Discover patterns & insights Statistics Perform basic statistics Table Functions Implement complex algorithms OLAP & Discoverer Interactive query & drill-down SQL Loader High performance data loader Web Services Standard communication between applications Merge/Upsert Enabling update and insert in one step TransportableTablespaces Rapidly exchange tables Oracle Streams Rule-based subscription for information sharing

  21. Oracle Life Sciences Platform Transparent Gateways Fast access using Oracle OCI Distributed Queries Perform searches across domains Generic Gateways Access any data using ODBC e.g. MySQL GenBank e.g. PubMed External Tables Ability to index and query external files UltraSearch Search external sites & repositories MySQL Toolkit Easily move MySQL data into Oracle Real Application Clusters Linear scalability Oracle Portal Build personalized portals Application Server Provide scalability for themiddle tier XML DB Flexibly manage data interMedia Store & manage images Security Enforce security Auditing Create audit trail to facilitate FDA compliance Workflow Automate laboratory & business processes Collaboration Suite Collaborate securely iFS/Files Share documents e.g. SwissProt SP-ML Extensibility Framework (Data cartridges), manage complex scientific dataLOBs Manage unstructured data Text Index & query text, e.g. literature searches Data Mining Discover patterns & insights Statistics Perform basic statistics Table Functions Implement complex algorithms OLAP & Discoverer Interactive query & drill-down SQL Loader High performance data loader Web Services Standard communication between applications Merge/Upsert Enabling update and insert in one step TransportableTablespaces Rapidly exchange tables Oracle Streams Rule-based subscription for information sharing

  22. 1. Access Heterogeneous Data UltraSearch External Sites Distributed query Flat files MySQL Sybase DB2 External Table Transparent Gateway Transparent Gateway Generic Connectivity MySQL Migration Toolkit DBlinks Transportable Tablespaces

  23. Oracle Transparent Gateways Integrate data from disparate systems Generic Connectivity ODBC/JDBC connectivity External Tables Access data from flat files Distributed Queries Query across multiple Oracle and heterogeneous data sources Transportable tablespaces Rapidly move tablespaces between Oracle databases SQL*Loader High performance data loader Oracle Streams Rule-based subscription for information sharing Dblinks Connectivity between databases UltraSearch Query range of data repositories (web sites, files, email, databases, etc.) Migration Toolkits Tools to facilitate movement of data into Oracle Merge / Upsert Update and insert in one step 1. Access Heterogeneous Data Flat files MySQL

  24. 2. Integrate a Variety of Data Types Genomics Proteomics Modeling Pathways Clinical Pharmaco- genomics Functional Genomics Chem-informatics Graphicmodified from original courtesy of Sun Microsystems

  25. 2. Integrate a Variety of Data Types • XML DB • Unite XML content and relational data • SQL & XML become one • LOBs • Manage unstructured data • Internet File System (Oracle Files) • Manage files and folders • Text • Index and query of text content & documents (Word, Powerpoint, HTML, Adobe PDFs, etc.) • interMedia • Manage audio, video and image data XML

  26. European Bioinformatics Institute (EBI) • Hosts major public databases (e.g. SwissProt, EMBL Nucleotide Sequence Database, Medline) on Oracle. (Total: > 5 TB) • Uses Oracle XML DB and Oracle Text for Medline – in development. • Size: 11 million records, 200 GB • Uses Oracle9i Database and Application Server.

  27. 2. Integrate a Variety of Data Types Oracle9i Server Extensibility Framework (Data Cartridges)- Manage complex scientific data

  28. Chemical Searching • Chemistry searching requires special techniques • Chemical name is not unique

  29. Chemical Searching • Chemistry searching requires special techniques • Chemical name is not unique “Viagra®”

  30. Chemical Searching • Chemistry searching requires special techniques • Chemical name is not unique “Viagra®” “sildenafil citrate”

  31. Chemical Searching • Chemistry searching requires special techniques • Chemical name is not unique “Viagra®” “sildenafil citrate” • Chemists think graphically

  32. Chemical Searching • Chemists think graphically • Chemistry searching requires special techniques • Chemical name is not unique “Viagra®” “sildenafil citrate” • The solution: • A graphical user interface • Specialized operators such as substructure search (“sss”) = a chemical “contains” finds

  33. MDL Discovery Framework A multi-tier system for managing and integrating discovery data and workflows Domain-specific application and database services and API Chemistry rules, drawing, and rendering Single application access to multiple DBs and services Key Advantages Integrate data sources across R&D Easily create web or client solutions Quickly adopt new tools and methods for development www.mdl.com Oracle Features Oracle 8i/9i Database Extensibility Option (chemical data cartridge) Replication support Oracle9iAS J2EE services MDL Information Systems, Inc.

  34. The ActivityBase Suite Capture, manage and use chemical and biological data in life sciences discovery Manage full range of disparate data types The leading application for drug discovery research worldwide Key Advantages Integration framework for cheminformatics and bioinformatics data Rich data context enables data quality Supports manual and automated data capture & management Maximizes the value of discovery data www.id-bs.com Oracle Features Chemistry cartridge (ChemXtra) PL/SQL stored procedures JAVA stored procedures XML Materialized views Data warehousing 9i compatible IDBS

  35. 3. Manage Vast Quantities of Data 500TB 450TB 400TB 350TB 300TB 250TB Data StorageToday 200TB 150TB 100TB 50TB 0 2002 1994 1995 1996 1997 1998 2003 2004 2005 2006 Jan-01 Oct-1999 Apr-2000 Nov-2001 • Grid support in Oracle 10g • Oracle Scales to Petabytes • Largest life sciences databases run Oracle • Oracle 80% market share - IDC • Partitioning • Divide and conquer • Oracle 10g Application Server • Provide scalability for middle tier • Oracle Data Guard • Protect data from human or system failures

  36. 3. Manage Vast Quantities of Data Support for Grid • Distributed queries, External Tables, Security, RAC • Grid Access to Oracle Utilities through Globus Resource Allocation Manager(GRAM) • Export, Import, SQLPlus • Grid Access to Oracle 10g Database • Invoke PL/SQL routines specified in Globus Resource Specification Language • Grid Resource Information Service (GRIS) for Oracle Database • Discover & monitor Oracle databases

  37. High-speed interconnect 3. Manage Vast Quantities of Data • Real ApplicationClusters (RAC) • Start with one server, one database and grow as you grow • Linear scalability out of the box • Save on Hardware and Storage costs Data Loads Proteomics Portal Sample/Lab • Works with ALLapplications • Fail-over transparent to users • Easy to administer A-Z

  38. Oracle 1. Add new node 2. Start instance on new node Oracle Real Application Clusters Works for All Applications No Code Change

  39. Oracle Real Application Clusters Greater Than 85% Scalability

  40. Genentech, Inc. • Leading biotech company • Over 2 TBs of data in Oracle • Oracle serves as a centralized information resource for gene searching and database cross-referencing. • Oracle used for the entire pipeline from research to clinical data to manufacturing and sales applications. • Key Advantages of Oracle • Improved performance • Greater reliability • Genentech's corporate goal is 99.999% availability in a 24x7 environment • Oracle Environment • Oracle 9i database • Real Application Clusters • Oracle9i Real Application Clusters provide the foundation for the scalable and highly available database infrastructure we require to meet our growing data demands in all areas of our business." --Scooter Morris, Genentech, Inc.

  41. High-Level Project Goals Manage data throughout every step of a complicated process Create a laboratory information management system (LIMS) enabling large scale sequencing Provide reliable back up and recovery of vast amounts of data Key Benefits Provided easy access and management for vast amounts of data Ensured scalability needed to accommodate future growth Oracle Environment Oracle Database Enterprise Edition Oracle9iAS Enterprise Edition "We trust Oracle in its ability to run terabyte-class databases in clustered environments with high availability. And we're pleased to say that Oracle has not disappointed us. "-- Toru Suzuki, Project Manager, Dragon Genomics Center, Takara Bio Inc. The Dragon Genomics Centerof Takara Bio Inc. The Dragon Genomics Center of Takara Bio Inc., specializing in large-scale sequencing, is among the highest speed genome-analyzing centers in Asia.

  42. Bioinformatics Center Institute for Chemical Research Kyoto University The Bioinformatics Center Institute for Chemical Research Kyoto University is leading biotechnology research thanks to its comprehensive studies in various areas, including the life sciences, information sciences, chemistry and physics. “In order to manage this massive amount of genetic information and to operate efficiently, it is essential to have a platform with paramount stability. Our web site receives accesses from all over the world continuously, 24 hours a day. In order to offer the latest information under such circumstances, performance is also an issue. In this sense, the Oracle Database was the most appropriate since it can handle this enormous amount of data in a fast and stable manner, 24 hours a day.” – Professor and Director Minoru Kanehisa, Bioinformatics Center Institute for Chemical Research Kyoto University

  43. 4. Find Patterns and Insights • Oracle Data Mining • Find relationships and clusters associated with healthy and diseased states • Naïve Bayes, Adaptive Bayes Networks, Attribute Importance, Association Rules, K-Means, O-Cluster, SVM, NMF algorithms • Data Mining for Java (DM4J) GUI wizards and results browser • Oracle Discoverer & Oracle OLAP • Interactive query & drill-down • Statistical functions • Perform basic statistics in Oracle • e.g. summary statistics, e.g. mean, stdev, median, quantiles, hypothesis testing, distribution fitting, correlations, linear regression • Oracle Text & Text Mining • Classify & cluster documents relevant to area of interest • Table Functions • Implement complex algorithms within the database

  44. 4. Find Patterns and Insights Life Sciences data Answer complex questions about the relationships in genomic, clinical and pharmacological data Deductive Analysis Functional Genomic Databases Clinical Databases InductiveAnalysis Proteomics Database Finding relationships for classification, class discovery and prediction Pharmacological databases

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