Genome Science Institute Faculty Meeting

AgendaTuesday June 15, 2010

3:00pm to 4:00pm

X715

Annual GSI Research Symposium2010 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 speakersSeeking suggestions on topics and target

audience

GSI Seed Grants ProgramProgress Reports for the 2009 awardsAnnouncement of 2010 awards

Graduate Program in Genetics and Genomics Update on current and incoming studentsIncreasing faculty participationCommittees (Seminars and recruitment)Teaching (Integrated Curriculum) Ph.D. student mentoring and rotations.

Enhancing Genetics and Genomics ResearchIncreasing GSI faculty and student participation Increasing and developing new research opportunitiesRecruiting new faculty

Symposium

2nd AnnualGenome Science Institute

Symposiumto be held

Wed Oct 6th 2010

- Anita Destefano

Symposium

Inaugural Symposium

• 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

• 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

Ingenuity Pathway Analysis

GSI sponsored Institutional License

IPA

- Anita Destefano

IPA

Transforms a list of genes into a set of networks

– 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

To date 23 users have logged on

Upgrade

IPA

Even with 23 active accounts we have not had more than 2 concurrent users

IPA

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

• 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)

  Total Usage (CPU-Years)

 Number Months

LinGA-II / RedStar

FramGen / BlueIce Total

Pre Merger 21 175.5 173.5 349.0

Post Merger 6.5 106.7 91.8 198.5

All Time /Increase   282.1 265.4 547.5

Average Monthly Usage (CPU-Months)

LinGA-II / RedStar

FramGen / BlueIce Total

100.2 98.2 198.5

196.6 169.4 366.0

96% 72% 84%

LinGA

Storage Usage

• > 15TB of active primary data– traditional backups fail

• > 90% utilization – snapshots are no longer safe

• Primary disc usage– doubled in last 6 months

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%

LinGA Expansion

2010 Expansion Goals

• 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 Solution5 performance blocks

48 TB raw / 32 TB usable 1 capacity block (remote site)

96 TB raw / 64 TB usable

Each block2 file serving nodes

2 x quad-core CPUs & 48 GB RAM each10GigE + 2 x GigE connections each

2 redundant RAID array controllers1 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 nodes2 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 nodes2 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

The LinGA documentation wiki can be found here:

http://collaborate.bu.edu/linga

Please visit to learn more about this resource

LinGA

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

Fall 2009/Spring 2010• 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 humandevelopment 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 2011October 19, Evan Eichler, Univ. of Washington

Investigator, HHMI

November 16, Victor Ambros, UMASS Med SchoolMember, National Academy of ScienceAlbert Lasker Award for Basic Medical Research (2008)Discovered the first known miRNA

December 7, Jeannie Lee, Mass General Hospital/Harvard Med.Investigator, HHMI2010 Molecular Biology Prize from the National Academy of Sciences

January 18, Ruth Lehmann, NYU Med SchoolInvestigator, HHMIDirector, The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the

Skirball Institute of Biomolecular MedicineMember, National Academy of Science

Seminar Series

GSI Seed Grants

- Rick Myers

GSI Seed Grants

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

2009 Awards - $50,000 total

GSI Seed Grants

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

2010 Awards - $40,000 total

Graduate Program in Genetics and Genomics

GPGG

- Shoumita Dasgupta

GPGG

Graduates in the past yearDorothy Pazin (Postdoctoral fellow, Harvard Dental School)Tovah Day (Postdoctoral fellow, Dana Farber)Ihnyoung Song (Postdoctoral fellow, UCSF)Kelly Graham (Postdoctoral fellow, Roswell Park Cancer Inst.) Gerald Stanvitch (Postdoctoral fellow, Geisinger Medical Center)

Seven current students5th year and beyond: Florin Crazin4th year: Constantina Christodoulou & Catalina Perdomo2nd year: Kristin Ott & Jessica Vick1st year: Sarah Kleinsorge & Becky Kusko

GPGG

Incoming Students Fall 2010

Carly Garrison B.S., Boston University

Elyse Kozlowski B.S., Rowan UniversityCurrently a technician in the Llinás lab at

Princeton

Hila Milo Rasouly B.S., Tel Aviv UniversityM.S., Genetic Counseling, Hebrew Univ.

GPGG

Increasing Faculty Participation

• 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 feedbackPlease send all feedback and suggestions to GSI@BU.EDU

We look forward to hearing from you.

-Anita, Kenn, and Rick