CCEGA VisionDan Reed

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Carolina Center for ExploratoryGenetic
AnalysisIntroduction and Context

• Dan Reed
• Dan_Reed_at_unc.edu
• Chancellors Eminent Professor
• Director, Renaissance Computing Institute
• University of North Carolina at Chapel Hill

Supported in part by NIH Grant 5P20RR020751-02
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Genetics and Disease Susceptibility
Phenotype 1 Phenotype 2 Phenotype 3
Phenotype 4
Ancestry Environment
Age Gender
Identify Genes
Pharmacokinetics
Metabolism
Endocrine
Biomarker Signatures
Physiology
Proteome
Transcriptome
Immune
Morphometrics
Predictive Disease Susceptibility
Source David Threadgill/Terry Magnuson
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The Data Wave

• Many sources
• sequencing
• microarrays
• environmental
• public health
• family studies
• clinical
• Many technology enablers
• increased detector resolution
• increased storage capability
• The challenges
• managing complexity
• tracking knowledge
• extracting insight

We Are Here!
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Data Heterogeneity and Complexity
Genomic, proteomic, transcriptomic, metabolomic,
protein-protein interactions, regulatory
bio-networks, alignments, disease, patterns and
motifs, protein structure, protein
classifications, specialist proteins (enzymes,
receptors),
Proteome
Source Carole Goble (Manchester)
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Convergence and Opportunity

• Center for Genome Sciences (CCGS)
• ten year investment of 245M
• new center and department
• 4 buildings and 22 faculty lines
• advanced facilities and equipment
• participation by multiple schools and departments
• 25M anonymous gift for proteomics
• Renaissance Computing Institute (RENCI)
• interdisciplinary applications of computing
• faculty, staff and student collaborations
• new infrastructure and capabilities
• technology transfer and economic development

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Information Visualization Challenges

• Heterogeneity and complexity
• data types
• numerical, non-numerical
• textual, graphical,
• sources and scale
• distributed databases, conferences
• journals, web pages,
• ontology and relationships
• metadata, meanings and connections
• Compatibility and collaboration
• from desktop to distributed and collaborative
• familiar tools and interfaces
• UNC tiled display wall deployment
• Health Sciences Library/RENCI collaboration
• HSL focus on fostering collaboration
• building renovation and redesign

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RENCI/Health Sciences Collaboration
June 2005
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PITAC Data and Software Repositories

• Findings
• Explosive growth in sensors and scientific
  instruments has engendered unprecedented volumes
  of data, presenting historic opportunities for
  major scientific breakthroughs in the 21st
  century
• Computational science now encompasses modeling
  and simulation using data from these and other
  sources, requiring data management, mining, and
  interrogation
• Recommendations
• Federal government must provide long-term support
  for computational science community data
  repositories
• defined frameworks, metadata structures
• algorithms, data sets, applications
• review and validation infrastructure
• Government must require funded researchers to
  deposit their data and research software in these
  repositories or with access providers that
  respect any necessary or appropriate security
  and/or privacy requirements

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Deep Carolina (Proposed)

• Features
• five year partnership timeline (minimum)
• RTP/UNC IBM anchors
• proximity facilitates collaboration
• joint faculty/staff participation
• leading edge computing infrastructure
• hardware and software
• Rationale
• leverage IBM and Triangle resources
• develop and evaluate new technologies
• explore applications of computing to new problems
• Joint resource commitments
• Carolina and IBM

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CCEGA Project Goals

• Develop collaborative experiences and plans
• preliminary data to apply for a P50 grant
• Deliverables and activities
• develop a protocol for prospective studies
• using ongoing studies as examples to define best
  practices
• Carolina Cohort
• develop a prototype informatics infrastructure
• data models, methods, tools and portals
• demonstrate the utility of data mining
• applied to established project(s)
• facilitate use of best practices for existing
  projects
• develop an environment for cross training and
  education
• formal and informal education touching project
  participants and trainees
• Foster mutual awareness and shared needs

Supported in part by NIH Grant 5P20RR020751-02
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CCEGA Vision
Interoperable Data Management
Faculty, Staff Students
Driving Problems
Promoting Mutual Awareness
Experimental Genetics Portal
Analysis Techniques
Statistical Computational Techniques
Extant Data Models
Virtuous Cycle
Interdisciplinary Research Education
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Tentative Science Requirements

• Integrated storage, analysis and exploration
• reusable infrastructure and shared capability
• Shared collaborative infrastructure
• new science and larger collaborations
• Leverage from other infrastructure
• distributed resource sharing and use
• Simplicity, simplicity, simplicity
• reduce redundant infrastructure construction
• focus time and talent on research

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CCEGA Participants

• Coordination team
• Dan Reed, RENCI
• Terry Magnuson, CCGS
• Alan Blatecky, RENCI
• Kirk Wilhelmsen, CCGS
• Eleven departments/institutes
• Biostatistics
• Cancer Center
• CCGS
• Computer Science
• Epidemiology
• Genetics
• Health Science Library
• Information and Library Science
• Pharmacy
• RENCI
• Statistics
• Campus wide support
• from many sources

• Project participants
• Brad Hemminger, Information Library Science
• James Evans, Genetics
• Kevin Gamiel, RENCI
• Xiaojun Guan, RENCI
• Barrie Hays, Health Science Library
• Clark Jefferies, RENCI
• Ethan Lange, Genetics
• Andrew Nobel, Statistics
• Karen Mohlke, Genetics
• Kari North, Epidemiology
• Susan Paulsen, Computer Science
• Fernando Manuel Pardo, Genetics
• Charles Perou, Cancer Center
• Lavanya Ramakrishnan, RENCI
• Jan Prins, Computer Science
• Patrick Sullivan, Genetics
• Lisa Susswein, Cancer Center
• David Threadgill, Genetics

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Formal CCEGA Activities

• Workshops
• genetics and disease
• analysis methods (today)
• Cross-disciplinary tutorials
• genotyping
• XML
• others to come
• Working groups
• ELSI, analysis and informatics
• Software prototyping
• portal and data model planning
• Management group
• planning and strategy

www.renci.org/P20
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CCEGA Working Groups/Structures

• ELSI
• IRB and coordinated data sharing
• James Evans, Genetics (lead)
• Exploratory analysis
• data mining and classification techniques
• Jan Prins, Computer Science (lead)
• Informatics
• LIMS, data models and representations
• Brad Hemminger, Information and Library Science
  (lead)
• Integration and prototyping
• portals, software and tools
• Xiaojun Guan, RENCI (lead)
• Organization and operation
• weekly meetings with posted topics
• web summaries for project access
• www.renci.org/P20

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Infrastructure and Data

• Bioinformatics portal
• standard tools and community interfaces
• data integration and access
• Large scale visualization and collaboration
• tiled display wall and tools
• Strawman data models
• discussion, data validation and tool development
• Simulated case control data sets
• no genotype/phenotype connection (null data)
• phenotype via simulated development process

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North Carolina Bioportal

• Goals and features
• standard interfaces
• common tools and databases
• extensibility mechanisms
• new tools, techniques and data
• authentication and security
• controlled access
• local and remote access
• national coupling and sharing
• Currently
• 100 standard applications
• Emboss, Glimmer, Hmmer
• NCBI, Phylip, other,
• growing suite of databases
• NCBI Blast, GenBank, GenPept
• PDB, Prints, rebase, Repbase
• Uniprot, Fasta, genomes, Pfam
• Prosite, Refseq, Transfac, WU Blast
• May 2005 initial release

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North Carolina Bioportal
Users
Account Management
BioPortal
MySQL databases
Grid Gatekeeper
MyProxy
GridFTP
OpenPBS
Applications
Application Databases
Pise

• Open Grid Computing Environment (OGCE)
• shared development
• standard web services
• adopting portal standards (JSR168)
• used by cyberinfrastructure projects
• LEAD, NEES, PACI, DOE, TeraGrid

Local cluster
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Our Vision of Success

• Local avatars for the national community
• driving problems and experiences
• infrastructure testing and validation
• Multidisciplinary collaboration
• biomedical and IT researchers
• software developers
• National infrastructure and communities
• distributed and federated
• customizable to local needs
• interoperable and shared
• The Virtual Observatory astronomy model
• standard tools
• metadata and data models
• virtual community

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Next Kirk Wilhelmsen