NCGR Bioinformatics Working Group

31 Pages·2016·3.55 MB·English

by  Faye Schilkey

NCGR Advanced Bioinformatics
Prepared for
University of Alaska, Fairbanks and Anchorage
January 28-29, 2016
Faye D. Schilkey
Director of Strategic Projects and
NM-INBRE Sequencing and Bioinformatics Core
Agenda
NCGR
q 
Education
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Research
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Sequencing Center
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Bioinformatics
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Understanding Projects at UA F & A
q
National Center for Genome Resources
501c(3) nonprofit research institute
Applies bioinformatics, software engineering and
next-generation sequencing to solve the
preeminent challenges of 21st century biology
NCGR History
1994 NCGR founded for discovery-driven
q 
computational biology and bioinformatics in
support of the DOE Human Genome Project
Created 1st relational human genome sequence database
q 
(GSDB)
1997-98 NCGR established and sold Molecular
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Informatics, now part of Celera Diagnostics
2000 NCGR’s completes new 32,000 square foot
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research facility
NCGR History (cont.)
2000-2007 NCGR continues innovative
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bioinformatics tool development
SYStem for Integrating heterogeneous bioinformatic
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resources (ISYS)
Comparative Map and Trait Viewer (CMTV)
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A metabolic database and discovery tool (PathDB)
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A tool for Genomic Exploration and Survey of Immune
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Response (GEYSIR)
The Arabidopsis Information Resource (TAIR)
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The Legume Information System (LIS)
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NCGR History (cont.)
2007 NCGR creates NM Genome Sequencing Center
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Alpheus created to analyze Next Gen Sequencing (NGS) data
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2007 – date, Major sequencing & analysis projects
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NIH NM-INBRE
§ 
Moore Foundation Marine Microbial Transcriptome
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Sequencing Project (MMETSP)
NSF Medicago HapMap project
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Cacao Genome project funded by Mars, Inc.
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Development of a human carrier screening test
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NOAA – Deep Well Horizon
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2014 NCGR develops Bioinformatics-in-a-BoxTM
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Faye D. Schilkey, BS
Computer Engineering
First Career:
q  Software engineering in automotive

(robotics) and aerospace (guidance and autopilot) systems
Second Career (Big Data):
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IT / Software Engineering / Database development in
n 
Genomics and Bioinformatics (20 yrs)
GSDB, ISYS, PathDB, GEYSIR
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PI/Director, NMINBRE Seq & Bioinformatics Core (10 yrs)
n 
Sequence Center operations, R&D, and product
n 
development (9 yrs)
Leverage sequencing and bioinformatics techniques to
n 
solve biological questions
Main elements of NCGR
Bioinformatics
Research Sequencing
Education
STEM / undergrad / grad
INBRE/NCGR Researcher/student impact
2004-2015 period > 2500 researchers/students positively impacted through SBC
activities
2015
2014
2013
Sequencing/bioinformatics for projects, pubs & grants (215)
2012
2011 College genomics/bioinformatics internships (125)
r 2010
a Pre K - grade 12 genomics/bioinformatics education (722)
e
Y
2009
BioInformatics, Science and Technology Symposium-NMBIST (1080)
2008
College genomics/bioinformatics seminars (525)
2007
2006
2005
2004
0" 100" 200" 300" 400" 500" 600" 700" 800"
Number of researchers and students impacted
Research at NCGR
•  Human health
•  Plant science and nutrition
•  > 200 publications
AJ Brass
Foundati
on