Genome Science Institute
Faculty Meeting
Agenda
Tuesday June 15, 2010
3:00pm to 4:00pm
X715
Annual GSI Research Symposium
2010 Symposium planning (tentatively scheduled
for October 6, 2010)
Ingenuity Pathway Analysis (IPA)
GSI supported license: capabilities and
limitations.
Linux Cluster for Genetic Analysis (LinGA)
Maintaining and expanding support and
capabilities.
Seminar Series
Seeking suggestions for compelling speakers
Seeking suggestions on topics and target
audience
GSI Seed Grants Program
Progress Reports for the 2009 awards
Announcement of 2010 awards
Graduate Program in Genetics and Genomics
Update on current and incoming students
Increasing faculty participation
Committees (Seminars and recruitment)
Teaching (Integrated Curriculum)
Ph.D. student mentoring and rotations.
Enhancing Genetics and Genomics Research
Increasing GSI faculty and student participation
Increasing and developing new research opportunities
Recruiting new faculty
Symposium
2nd Annual
Genome Science Institute
Symposium
to be held
Wed Oct 6th 2010
- Anita Destefano
Symposium
Inaugural Symposium
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Very Successful!!
Was held Oct 2009
63 abstracts submitted
6 selected for oral presentations
– 2 undergrad
– 2 grad
– 2 postdoc
• 8 poster awards
– 5 grad
– 3 post doc
Symposium
2nd Annual GSI Symposium
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Save the Date: Oct 6th 2010
Look for call for abstracts in the Fall
Encourage your students and postdocs to participate
We did receive feedback after 2009
Send suggestions regarding symposium to:
– gsi@bu.edu
IPA
Ingenuity Pathway Analysis
GSI sponsored Institutional License
- Anita Destefano
IPA
Transforms a list of genes into a set of networks
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Based on Ingenuity Pathways Knowledge Base
Abstracted to Global Molecular Network
Identifies focus genes from your list
Identifies signaling and metabolic pathways, molecular networks, and
biological processes
IPA
IPA
Institutional License
• Upgrade of existing license for 5 user accounts
• Unlimited number of users may register
– Requires @bu.edu email address
• 3 concurrent users allowed until Oct 1, 2010
• 1 concurrent user after Oct 1, 2010
• To obtain account visit
http://www.bumc.bu.edu/gsi/ingenuity-ipa
Or email gsi@bu.edu
IPA
Upgrade
To date 23 users have logged on
IPA
Even with 23 active accounts we have
not had more than 2 concurrent users
IPA
• Will continue to advertise the resource
• Are working with IPA to schedule a training session in next
couple of months
• Monitoring usage reports
• Will solicit feedback regarding usefulness to researchers
• Other resources??
LinGA
Linux Cluster for Genetic Analysis
- Andi Broka
LinGA
Last Months Usage
LinGA
Overall Usage / Utilization
Average Monthly Usage (CPU-Months)
Total Usage (CPU-Years)
Number
Months
LinGA-II /
RedStar
FramGen /
BlueIce
Total
LinGA-II /
RedStar
FramGen /
BlueIce
Total
Pre
Merger
21
175.5
173.5
349.0
100.2
98.2
198.5
Post
Merger
6.5
106.7
91.8
198.5
196.6
169.4
366.0
282.1
265.4
547.5
96%
72%
84%
All Time
/Increase
• Total Usage since move to Crosstown
– 4,799,876 CPU-Hours (548 CPU-Years)
• Current average monthly usage
– 267,355 CPU-Hours (366 CPU-Months)
LinGA
Storage Usage
Last Full Backup
November 15, 2009
17 TB
43%
Peak Usage
May 24, 2010
39 TB
98%
Current Usage
June 15, 2010
36 TB
92%
• > 15TB of active primary data
– traditional backups fail
• > 90% utilization
– snapshots are no longer safe
• Primary disc usage
– doubled in last 6 months
LinGA Expansion
2010 Expansion Goals
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Increase storage capacity
Address backup needs
Remote site replication
Increase number of high memory nodes
Scalable performance improvements
Maximize usable life of existing resources
Minimize cost
Allow room for future expansion
LinGA Expansion
Contributing Groups
• DOM (Largest share of funding)
• Atwood (Framingham, FOG)
• Cupples (Biostatistics)
• Farrer
• Neurogenetics
• Spira
• Steinberg
LinGA Expansion
HP StorageWorks X9000
Network Storage Systems
LinGA Expansion
X9320 Performance Building Block
LinGA Expansion
Storage Solution
5 performance blocks
48 TB raw / 32 TB usable
1 capacity block (remote site)
96 TB raw / 64 TB usable
Each block
2 file serving nodes
2 x quad-core CPUs & 48 GB RAM each
10GigE + 2 x GigE connections each
2 redundant RAID array controllers
1 GB of cache each
Total 336 TB raw / 224 TB usable
* Possibility to incorporate some of our existing storage
LinGA Expansion
Why is Storage Expensive?
LinGA Expansion
Compute Nodes
4 High Memory nodes
2 x quad-core Nehalem, 2.26 GHz each
2 with 144 GB of RAM each
2 with 72 GB of RAM each
12 High Density nodes
2 x quad-core Nehalem, 2.26 GHz each
64 GB of RAM each
Total
128 new cores (20% increase)
1.2 TB of RAM (73% increase)
LinGA Expansion
HP ProLiant SL2x170z
LinGA Expansion
HP ProLiant SL160z
LinGA
The LinGA documentation wiki can be found
here:
http://collaborate.bu.edu/linga
Please visit to learn more about this resource
GSI Seminar Series
- Kenn Albrecht
Seminar Series
• Goals:
– Invite internationally recognized extramural speakers at the vanguard of genetics
and genomics research
– Sponsor intramural speakers to forge interactions and collaborations among
Boston University investigators
• Committee:
– Members: Sam Thiagalingham, Mayetri Gupta, Zhijun Luo, Kenn Albrecht
* Additional members needed
• Schedule:
– Semimonthly, first and third Tuesday
• Time and place
– 3:00-4:00 pm, X714-715
• All seminars are webcast: see GSI website for details
Seminar Series
Fall 2009/Spring 2010
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Deep sequencing using the Illumina Genome Analyzer, llumina, Inc.
Genome Scans in Cancer; Common Variants, and What They Mean, Bruce Ponder, U. Cambridge
Epistasis and its Implications for Personal Genetics, Jason Moore, Dartmouth Medical School
Applications of 454 Sequencing to Healthcare Research, 454 Life Sciences
Genomic Analysis of C. elegans Development, Valerie Reinke, Yale University
Beyond PubMed and BLAST: Exploring NCBI tools and databases, Kate Bronstad & David Flynn, BUSM
Library
An Atlas of open chromatin spanning Diverse Human Cell Types in Health and Disease, Jason Lieb, U. of
North Carolina
Epigenetic profiles, asbestos burden, and survival in pleural mesothelioma, Karl T. Kelsey, Brown U.
Long-range gene regulatory architecture of the human genome, Job Dekker, UMASS Medical School
Genomics of Lung Development and Disease, Carol Bult, The Jackson Laboratory
Utilization of mouse mutagenesis and strain variation to understand human development and disease,
David Beier, Brigham and Women’s Hospital
The Epigenetic Basis of Common Human Disease, Andrew Feinberg, Johns Hopkins School of Medicine
Seminar Series
Fall 2010/Spring 2011
October 19, Evan Eichler, Univ. of Washington
Investigator, HHMI
November 16, Victor Ambros, UMASS Med School
Member, National Academy of Science
Albert Lasker Award for Basic Medical Research (2008)
Discovered the first known miRNA
December 7, Jeannie Lee, Mass General Hospital/Harvard Med.
Investigator, HHMI
2010 Molecular Biology Prize from the National Academy of Sciences
January 18, Ruth Lehmann, NYU Med School
Investigator, HHMI
Director, The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the
Skirball Institute of Biomolecular Medicine
Member, National Academy of Science
GSI Seed Grants
- Rick Myers
GSI Seed Grants
2009 Awards - $50,000 total
1. “Changes in Chromatin Accessibility of the Distal and Proximal IL1RL1 Promoter Upon Activation:
Dependence on Cell Type“
Ellen O. Weinberg, PhD, Cardiovascular Proteomics Center
Barbara Nikolajczyk, PhD, Department of Microbiology
2. “Role of microRNAs in thyroid carcinogenesis”
Jennifer Rosen, MD, Section of Surgical Oncology
Stephanie L. Lee, PhD, Section of Endocrinology, Diabetes & Nutrition
Antonio de las Morenas, MD, Department of Pathology & Laboratory Medicine
3. “Possible functional diversification of the CP2 and p53 protein families from a common ancestor
early in animal evolution—Evidence from the basal animal model, Nematostella vectensis”
John R. Finnerty, PhD, Department of Biology
Ulla Hansen, PhD, Department of Biology
Zhi-Xiong Jim Xiao, PhD, Department of Biochemistry
4. “Integrating genetics and genomics of COPD”
Jemma B. Wilk, DSc, Department of Neurology
Avrum Spira, MD, MSc, Section of Pulmonary, Critical Care & Allergy Medicine
GSI Seed Grants
2010 Awards - $40,000 total
1. “Epigenomic regulation of maturation of the phenotype of basal forebrain cholinergic neurons“
Jan Krzysztof Blusztajn, Department of Pathology & Laboratory Medicine
James E. Galagan, PhD, Biomedical Engineering, Microbiology
2. “Role of microRNAs in epigenetic imprinting by testosterone”
Ravi Jasuja, PhD, Endocrinology, Diabetes & Nutrition
Hyeran Jang, PhD, Endocrinology, Diabetes & Nutrition
Avrum Spira, MD, MSc, Translational Bioinformatics Program
Shalender Bhasin, MD, Endocrinology, Diabetes & Nutrition
3. “Mechanism of deregulation of cellular signaling by infecting leukemia virus”
Sajal K. Ghosh, PhD, Cancer Research Center
Remco A. Spanjaard, PhD, Dept. Surgery & Otolaryngology
GPGG
Graduate Program in Genetics and Genomics
- Shoumita Dasgupta
GPGG
Graduates in the past year
Dorothy Pazin
Tovah Day
Ihnyoung Song
Kelly Graham
Gerald Stanvitch
(Postdoctoral fellow, Harvard Dental School)
(Postdoctoral fellow, Dana Farber)
(Postdoctoral fellow, UCSF)
(Postdoctoral fellow, Roswell Park Cancer Inst.)
(Postdoctoral fellow, Geisinger Medical Center)
Seven current students
5th year and beyond:
4th year:
2nd year:
1st year:
Florin Crazin
Constantina Christodoulou & Catalina Perdomo
Kristin Ott & Jessica Vick
Sarah Kleinsorge & Becky Kusko
GPGG
Incoming Students Fall 2010
Carly Garrison
B.S., Boston University
Elyse Kozlowski
B.S., Rowan University
Currently a technician in the Llinás lab at Princeton
Hila Milo Rasouly
B.S., Tel Aviv University
M.S., Genetic Counseling, Hebrew Univ.
GPGG
Increasing Faculty Participation
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Ph.D. student mentoring and rotations
Committees
Integrated First Year Doctoral Curriculum and Teaching
Participation in student activities such as
• Research in Progress Seminars
• Journal Club
• Currently 2nd and 4th Friday each month at noon
If you are interested in joining the GPGG contact
Shoumita Dasgupta: dasgupta@bu.edu
Genetics and Genomics
Enhancing Genetics and
Genomics Research
• Increasing GSI faculty and student participation
• Increasing and developing new research opportunities
• Recruiting new faculty
Genetics and Genomics
Identifying Impediments
• Where do we want to go?
• How do we get there?
• Faculty feedback
Please send all feedback and
suggestions to GSI@BU.EDU
We look forward to hearing from you.
-Anita, Kenn, and Rick