INBRE Bioinformatics in Research and Education at IDeA Institutions

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INBRE Bioinformatics in Research and Education
at IDeA Institutions Krishan K. Arora,
Ph.D. Division of Research Infrastructure Nationa
l Center for Research Resources National
Institutes of Health Department of Health and
Human Services October 26, 2005
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Division of Research Infrastructure
Institutional Development Award Program (IDeA)

• IDeA Program established in 1993
• Authorized in NIH Revitalization Act of 1993
• Congressional intent to enhance geographical
  distribution of research funds and increase
  research capacity
• Comparable to NSF Experimental Program to
  Stimulate Competitiveness in Research (EPSCoR),
  established in 1980
• IDeA Eligible 23 states and Puerto Rico

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Division of Research Infrastructure
Institutional Development Award Program

• Initiatives
• COBRE - Center of Biomedical Research Excellence
• INBRE - IDeA Networks of Biomedical Research
  Excellence (previously BRIN)
• IDeANet - Western BRIN Infonet (Lariat)

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Division of Research Infrastructure
Institutional Development Award Program

• COBRE Centers of Biomedical Research Excellence
  
• Purpose
• To build a multidisciplinary research center at
  doctoral institutions or research institutes
• Center Characteristics
• Development of a thematic scientific focus
• Led by an established investigator, funded by
  NIH, NSF or other comparable Federal or
  private sector source
• Comprised of 3 to 5 research projects each
  supervised by a junior investigator Requires
  bioinformatics core
• Must describe a clear plan for mentoring, career
  development, graduation and replacement of
  junior investigators

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IDea Networks of Biomedical Research Excellence
(INBRE)

• INBRE Goals (2004)
• To develop a statewide multi-disciplinary
  research network of doctoral degree granting and
  undergraduate institutions.
• To build and increase the research capacity by
  supporting faculty, fellows and students at
  participating institutions.
• To provide undergraduate faculty and students
  research support, serve as pipeline to health
  research careers.
• To provide outreach to students at undergraduate
  institutions, community colleges and tribal
  colleges.
• To enhance statewide science and technology
  knowledge base.

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IDeA Networks of Biomedical Research Excellence
(INBRE)

• 23 statewide networks
• Research-intensive institution(s)
• Bioinformatics core
• Outreach core
• Undergraduate institutions
• Outreach institutions
• Minority-serving institutions

MT
DE
SC
KS
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What is Bioinformatics for INBRE at IDeA-Funded
Institutions?

• Research
• Training and Education Opportunities
• Communications

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What is Bioinformatics for INBRE at IDeA-Funded
Institutions?

• Research
• Genomics and Proteomics data management
• Molecular Modeliing
• In Silico Biology
• Sequence Analysis
• Gene Expression Analysis
• Imaging
• Data Mining
• Computing at high speed, high capacity
• Archiving of databases
• Specialized equipment access (virtual
  laboratories) and collaborations between
  laboratories and investigators

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What is Bioinformatics for INBRE at IDeA-Funded
Institutions?

• Training and Education Opportunities
• Online courses Degree programs in bioinformatics
• Training in the tools and techniques used for
  data collection, management, analysis and
  others
• Pipeline to research-intensive institutions
• Outreach to undergraduate, tribal and community
  colleges
• Communications
• E-mail and basic computer services
• Library access
• Video teleconferencing

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IDea Networks of Biomedical Research Excellence
(INBRE)

• Bioinformatics Core
• Each State Network is set up to meet its
  needs
• For Example,
• KS Telecommunication to undergraduate
  institutions
• WY Reaching out tribal colleges
• AR Developing new training and degree programs
• NM Telecommunication Resources and tools
• MS Providing latest bioinformatics tools
• DE Tools Advanced visualization system - CAVE

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Delaware INBRE Bioinformatics at Delaware
Biotechnology Institute
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Delaware INBREDBI BioIT Infrastructure

• Systems
• Computation Cluster SunFire V60x Linux - 256
  CPUs
• Ranked 218 worldwide in November 2003
• Database Server SunFire 4800, 12 CPUs, 2.5 Tb
  disk
• Visualization Server SGI Prism, 8 CPUs, 1.2
  TByte
• 105ft2 FakeSpace CAVE Visualization Studio
• Software
• Databases Oracle, EST Data, MPSS, GenBank, NCBI
  Mirrors
• Analysis Tools SeqWeb GCG, Vector NTI,
  Sequencher
• Visualization Tools Amira, Volume Explorer,
  Starlight
• Custom Tools
• Research Personnel
• BioIT Staff
• Faculty
• PostDocs
• Students

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Delaware INBRE Statewide Bioinformatics Network

• Delaware State University
• Sun Fire V880 Server
• 6 SunBlade 100 Workstations
• 6 Dell Workstations
• Dedicated Space in Biotech Lab
• Delaware Tech
• 22 PC Workstations Server
• 2 SGI Fuel Workstations with MiniCAVEs
• Dedicated Lab
• Wesley College
• 10 PC Workstations Server
• Dedicated Lab
• Christiana Care
• SGI Fuel Workstation for
• Biomedical Visualization
• and MiniCAVE

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Delaware INBRE DBI CAVE 3D Visualization Studio

• FakeSpace 105 ft2 rear-projected 3D Workwall
• SGI Prism Server and Netframe 600 PC Server
• Immersive Environment with Ultrasound Tracking
• Supported by NIH-NCRR under BRIN/INBRE

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Delaware INBRE Biomedical Visualization Research
Analysis of Liver Tumor in Human Patient
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Research Networksconnectivity infrastructure
Network connectivity a key to collaboration
videoconferencing and other types of virtual
meetings and to handle the large volumes and
complexity of biomedical data.
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Research NetworksIDeANet Testbed (the Lariat
Project)

• Goals
• Provide increased connectivity for
  high-bandwidth science applications
• in the six western IDeA states MT, ID, AK, HI,
  WY, NV
• Facilitate collaborations among institutions

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January 10, 2005- University of Hawaii
demonstrates Hawaiis first 10 Gbps connection
outside the state, including a remote microscopy
demo linking Lariat participants in Manoa to the
National Center for Microscopy and Imaging
Research (NCMIR) in San Diego, CA
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IDeANet - Expanding Research Networks

• Link IDeA, RCMI (Research Centers in Minority
  Institutions) centers networks to each other
  and to research centers across the nation, around
  the world
• Stimulate and enhance collaborations with the
  broader biomedical behavioral research
  community, promoting interdisciplinary
  interactions and team science
• Enable broad access to key resources at IDeA,
  RCMI sites

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Some of NIH-Supported Bioinformatics Resources
and Initiatives
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NIH National Library of MedicineNational
Center for Biotechnology Information

• http//www.ncbi.nlm.nih.gov/
• Established in 1988 as a national resource for
  molecular biology information, NCBI creates
  public databases, conducts research in
  computational biology, develops software tools
  for analyzing genome data, and disseminates
  biomedical information - all for the better
  understanding of molecular processes affecting
  human health and disease.

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NIH Roadmap Initiative Re-engineering the
Clinical Research Enterprise NECTAR National
Electronics Clinical Trials And Research network

• http//www.nihroadmap.nih.gov
• NECTAR will provide the informatics
  infrastructure that will serve as the backbone
  for interconnected and inter-operable research
  networks in the area of clinical research.

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NIH National Center for Research Resources
Biomedical Informatics Research Network - BIRN

• http//www.ncrr.nih.gov/biotech/btbirn.asp
• This NCRR-supported initiative aims to bring
  together groups of centers, known as testbeds, to
  collaborate closely towards a unified scientific
  goal.
• The initial goal is to address the needs of
  biomedical investigators across the country to
  effectively share and mine data in a
  site-independent manner for both basic and
  clinical research.
• Currently the BIRN involves a consortium of 21
  universities and 30 research groups that
  participate in one or more of three test bed
  projects centered around brain imaging of human
  neurological disorders and associated animal
  models.

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NIH National Institute of General Medical
SciencesCenter for Bioinformatics and
Computational Biology

• http//www.nigms.nih.gov/Initiatives/CompBio/
• CBCB supports research and research training in
  areas that combine biology with the computer
  sciences, engineering, mathematics, and physics.
• The Center develops and manages programs in
  several areas of computational biology, such as
• computational genomics
• cell modeling
• molecular modeling and simulation
• biomedical software development
• high-throughput data analysis
• analysis of complex biological systems, and
• database design and enhancement
• The Center also collaborates with other NIH
  components and federal agencies in developing
  policies in this area.

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NIH National Cancer Institute cancer
Biomedical Informatics Grid, caBIG

• http//cabig.nci.nih.gov/
• caBIG a voluntary network or grid, is being
  developed under the leadership of the National
  Cancer Institutes Center for Bioinformatics.
• Goal is to speed the delivery of innovative
  approaches for the prevention and treatment of
  cancer. The infrastructure and tools created by
  caBIG also have broad utility outside the cancer
  community.