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

Welcome to the Oracle Life Sciences User Group Meeting Oracle HQ Bldg 350 Conference Center Redwood Shores, CA September 10 th, :30 am-7:30 pm

Oracle Life Sciences Day & User Group Meeting Agenda 8:00-8:30Breakfast 8:30-8:45 Welcome 8:45-9:45Oracle's Platform for Life Sciences - New 10G Features Preview & Solicitation Process for Features in Next Release Charlie Berger, Oracle Corporation 9:45-10:30New In Silico Drug Discovery Integrated Demo Joyce Peng, Oracle Corporation 10:30-10:50Break 10:50-11:30European Bioinformatics Institutes (EBI), Peter Stoehr Managing Scientific Literature (Medline) and XML Data Within Oracle 11:30-12:10The Wellcome Trust Sanger Institute, Martin Widlake Implementing a Terascale Data Store (20 TB) 12:10-1:00Lunch & Wish List Feature Post-it Notes 1:00-1:40Wyeth Research, Peter Smith 21 CFR PART 11 via Oracle Auditing at Wyeth

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

"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 Oracle’s Commitment

Life Sciences Value Chain Discovery Contract Research Organization Research Organization Hospital Pharmaceutical Mfg. Plant Pharmacy Distribution Development Manufacturing, Sales and Marketing PharmaceuticalCompany Regulatory Agency Clinical Trials Biotech / Pharmaceutical Research Labs Public/ Private Data Wet Lab In Silico Sample Data Biomedical Firm PharmaceuticalCompany Pre-Clinical Trials

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

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

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

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

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

0 50TB 100TB 150TB 200TB 250TB 300TB 350TB 400TB 450TB 500TB Life Science Challenge Exploding Volumes of Data “To meet the scientific goals we believe we need to add around TB of storage each year for the next 5 years” P. Butcher, The Sanger Centre Oct-1999 Apr-2000 Nov-2001 Jan Data Storage Today

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

Life Science Challenge Just A Few Biological Databases

Life Science Challenge Typical Research Environment Industrial Research Lab Public Databases Private/Service Databases Local Copies Partner or Collaborator Local Databases Find Patterns and insights Managevastquantities ofdata Collaborate securely Accessheterogeneous Data Accessheterogeneous data Integratea variety of datatypes

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

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

Genomics Proteomics Pathways Cheminformatics Clinical 1.Access heterogeneous data 2.Integrate a variety of data types 3.Manage vast quantities of data 4.Find patterns and insights 5.Collaborate securely Oracle’s Platform for Life Sciences

Oracle Life Sciences Platform Find Patterns and insights Managevastquantities ofdata Collaborate securely Accessheterogeneous Data Accessheterogeneous data Integratea variety of datatypes

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

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

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

 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, , databases, etc.)  Migration Toolkits – Tools to facilitate movement of data into Oracle  Merge / Upsert – Update and insert in one step Flat files MySQL

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

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.

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

 Chemistry searching requires special techniques – Chemical name is not unique Chemical Searching

 Chemistry searching requires special techniques – Chemical name is not unique “Viagra ® ” Chemical Searching

 Chemistry searching requires special techniques – Chemical name is not unique “Viagra ® ” “sildenafil citrate” Chemical Searching

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

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

MDL Information Systems, Inc.  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   Oracle Features – Oracle 8i/9i Database Extensibility Option (chemical data cartridge) – Replication support – Oracle9iAS J2EE services

IDBS  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   Oracle Features – Chemistry cartridge (ChemXtra) – PL/SQL stored procedures – JAVA stored procedures – XML – Materialized views – Data warehousing – 9i compatible

 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 3. Manage Vast Quantities of Data

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

High-speed interconnect 3. Manage Vast Quantities of Data –Works with ALL applications –Fail-over transparent to users –Easy to administer Real Application Clusters (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 Sample/LabProteomicsPortal A-Z

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

Oracle Real Application Clusters Greater Than 85% Scalability

 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 % 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. Genentech, Inc.

The Dragon Genomics Center of Takara Bio Inc.  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 Center of Takara Bio Inc., specializing in large-scale sequencing, is among the highest speed genome-analyzing centers in Asia.

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

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

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