Oracle PharmaGRID Response. Dave Pearson Oracle Corporation UK

Transcription

1 Oracle PharmaGRID Response Dave Pearson Oracle Corporation UK

2 Grid Concepts and Vision! Everything is a service! Resource virtualisation and sharing Hardware, storage, network, data, function, instruments & devices! Quality of service through unlimited resources RAMPS Optimisation! Scheduling! Load balancing! Collaborative working! No centralised control Discovery, introspection, negotiated access! The Grid is potentially the enabler for Utility Computing But there are some issues

3 Concerns Raised By PharmaGRID! Current Grid capabilities versus the vision! Grid services versus web services! Standards maturity! Grid middleware Robustness Interface stability! Quality of service Security, privacy, anonymity Reliability, availability, manageability, performance, scalability! Grid value proposition Difficult to justify deploying Grid today

4 Oracle Grid Position! Drive to Utility Computing makes the Grid unstoppable! Oracle will support emerging standards! Oracle is Grid enabling its products Core technology stack already supports key Grid concepts! Virtualisation, failover, load balancing, provisioning 10i will deliver enhanced Grid capabilities! Oracle stack will be self sufficient in Grid environment! Grid capabilities can be exposed through other vendor offerings

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

6 Oracle s Platform for Life Sciences Genomics Proteomics Cheminformatics Pathways 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

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

8 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 Flat files MySQL! 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

9 2. Integrate a Variety of Data Types Genomics Proteomics Modeling Pathways Clinical Functional Genomics Pharmacogenomics Cheminformatics Graphic modified from original courtesy of Sun Microsystems

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

11 2. Integrate a Variety of Data Types Extensibility Framework (Data Cartridges) - Manage complex scientific data Data Cartridge Oracle8i Oracle9i Server Service Interfaces Extensibility Interfaces Type System Server Query Processing Execution... Data Indexing Database Extensibility Services

12 2. Ask relevant questions Find me any compound that looks like my current structure, and that has been tested on any assay in my company where the IC50>200nM, where I know that I have a unique patent position, and hasn't been published in any journal? Oracle9i select c.id, p.structure, from compound c, protein p, assay a where a.compound_id = c.id and a.protein_id = p.id and a.company = BIO_SYS and a.ic50 > 200nM and similar_to(p.id, protein kinase ) and not_published(p.id, Medline ) and extract_value(value(p.id), Dgene/Protein/Id ) = p.id Message XML Text Relational Image

13 3. Manage Vast Quantities of Data! Oracle9i Scales to Petabytes Largest life sciences databases run Oracle Oracle 80% market share - IDC! Partitioning Divide and conquer! Oracle9i Application Server Provide scalability for middle tier! Oracle Data Guard Protect data from human or system failures! Support for Grid Concepts Data Storage Today Oct-1999 Apr-2000 Nov-2001 Jan TB 450TB 400TB 350TB 300TB 250TB 200TB 150TB 100TB 50TB 0

14 3. Manage Vast Quantities of Data 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 Proteomics Portal Sample/Lab Works with ALL applications Fail-over transparent to users High-speed interconnect Easy to administer A-Z

15 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 and O-Cluster algorithms! Data Mining for Java (DM4J) GUI wizards and results browser! Oracle Discoverer & Oracle OLAP Interactive query & drill-down! Statistics Perform basic statistics in Oracle! e.g. mean, stdev, median, correlations, linear regression! Oracle Text & Text Mining Classify documents relevant to area of interest! Table Functions Implement complex algorithms within the database

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

17 5. Collaborate Securely! Oracle Collaboration Suite - Integrated communications Single enterprise search across all repositories! Internal & external Flexible access! Web, desktop! Wireless and telephone

18 5. Collaborate Securely! Oracle9iAS Portal Build personalized portals! Oracle Workflow Automate laboratory and business processes! Oracle 9iFS Enable content management and collaboration! Revision control, check-in/check-out, access control! Virtual Private Database Different users have unique access privileges! Auditing Create audit trail to facilitate FDA compliance! Oracle9iAS Web Services Standard way to collaborate through the web

19 Oracle9i Unbreakable Security! Complete data protection! Manage user access! Detect data misuse with Auditing! Facilitate regulatory compliance (HIPPA, 21 CFR PART 11)! Proven against 15 independent evaluations

20 Grid Value Proposition! Today Focus on increased return on assets Increase information sharing! Longer term value proposition Responsiveness to change through virtualisation Resource provisioning New classes of application! Service composition! Dynamic assembly! Reuse Virtual organisations! Dynamically configured infrastructure! Collaborative working

21 Conclusions! The Grid is at the same state as the WWW 12 years ago! You can deploy Grid capabilities today using current Oracle technology Grid in a box! Oracle RAC Lintel/Blades is an ideal platform for building Grid infrastructure! Oracle will support emerging Grid standards! The vision is Utility computing

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