Building Technology Infrastructure and Sustaining It into the Future

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Building Technology Infrastructure and Sustaining
It into the Future Judith Van Houten Director,
Vermont Genetics Network (Vermont INBRE) and
Vermont EPSCoR October 23, 2008 NERLSCD Meeting
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IDeA Institutional Networking for Biomedical
Research Excellence (INBRE) Awards are intended
to build biomedical research infrastructure.
Infrastructure can be many things undergraduate
or K-12 programs for workforce development,
career development of faculty and graduate
students, hardware acquisition, renovations,
among other things. I will focus today on the
facilities infrastructure in the Vermont Genetics
Network (VGN).
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• Highlight How We Built Two New VGN Facilities
• Microarray and Proteomics
• In the beginning
• Determine Need
• Find Talented Staff
• Make a Plan for Service
• Build a user base
• Evaluate Impact on
• Funding Competitiveness
• Outreach Programs
• Plan for the future

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• First Step for VGN Microarray Facility
• Ascertain the need for a Microarray Facility.
• Demand is not always the same as need for
  research competitiveness.
• Outside consultants helped us to determine the
  need in Vermont and then helped us to decide on
  the platform and services to start our
  Microarray Facility.

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Step Two Find the best staff

• The most important thing you can do to make a new
  facility succeed is to recruit the best, talented
  staff who are
• service-oriented and like to work with
  researchers as collaborators
• willing to work in a collaborative team
• creative and want to learn as the field and its
  technology expand
• networking with peers and industry reps

Tim Hunter and Scott Tighe
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Next Steps Plan for the service from sample
preparation to data analysis Work flow
Quality control Quality publishable data To
insure good outcomes Control over sample
preparation Assist in Experimental
Design Provide data analysis support -Crucial for
high quality data that are publishable! Web
based as much as possible Database for
Assessment and Reporting
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From the VGN Microarray Website
UVM Microarray Facility at the University of
Vermont The UVM Microarray Facility staff
provides comprehensive support to all projects
submitted including RNA extraction techniques,
RNA concentration, and other issues that can
present regarding upfront preparation of samples.
Microarray Brochure (Mission, Access Guidelines
and Prices) Guidelines for Facility Access and
Sample Submission Step 1 Initial Consultation
All investigators who wish to pursue a project
through the facility are strongly encouraged to
meet with the Microarray and Bioinformatics
Facility staff together to ensure proper
experimental design and a clear understanding of
sample requirements for processing through the
facility including turnaround times. Please
contact Tim Hunter at 656-2557 or Jeff Bond at
656-4068 to arrange a consultation meeting.
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Step 2 Submit Total RNA samples for quality
assessment .The facility staff will meet to
discuss results and a report including traces
will be given back to the investigator and
consulted how to proceed. Once you have submitted
your samples for Bioanalyzer chip analysis, you
are considered to be in the queue for target
preparation. Step 3 Submit RNA samples for
Target prep. . Step 4 Test Chip
Hybridization and Scanning. We recommend a
representative test chip be run for each batch of
target preparations. ..An experiment report will
be provided to the investigator. Step 5
Hybridization and scanning of target chip. A CD
will be provided to the investigator Step 6
Data Analysis Detailed analysis is the
responsibility of the investigator in
collaboration with the Bioinformatics Core
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• Next Step
• Developing the User Base and Loyal Clientele
• Early Success
• Early Low or No Fees
• Seminars and Education Outreach to the Research
  Community
• Celebrating our successes
• Continuing Education of the Staff
• Finding New Ways to Save on Client Fees
• Surveys and assessment

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Impact Grant Year 3 2007-08 Experimental design
consultations with 16 investigators Completion
of 27 microarray projects (292 GeneChips) Perform
ed 93 RNA assessments 59 PicoChips, 118
NanoChips, 3 small RNAs chip (new service,
implemented, August, 2008)
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2007-2008
Impact 2007-08 Publications (8) Grant
Applications Trained graduate students,
postdocs, techs Seminars presentations
(11) Support of Outreach Programs Assessment Quant
itative Data Survey results
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MICROARRAY OUTREACH
Tim Hunter and Scott Tighe
2007-2008 Green Mt. College Marlboro
College Norwich University Middlebury
College Johnson State Castleton State Saint
Michaels College
Janet Murray and Pat Reed
Microarray Research is so user-friendly at UVM
that we take it into college lab classes all
across the state in our Outreach Program!
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Bioinformatics Core is essential to the success
of the Microarray Facility Front end consulting
for experimental design Data Analysis
Jim Vincent
Bryan Fleming
Rama Kocherlakota
Jeff Bond
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Bioinformatics Core is essential to the success
of the Proteomics Facility Front end consulting
for experimental design Data Analysis
Jim Vincent
Bryan Fleming
Jeff Bond
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• Proteomics Facility
• In the beginning
• Determine Need
• Find Talented Staff
• Make a Plan for Service
• Build a user base
• Evaluate Impact on
• Funding Competitiveness
• Outreach Programs
• Plan for the future

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Proteomics Facility

• Establish Level of Need
• Need for MS for protein analysis was clear from
  meetings with faculty members from around the
  State.
• Meetings helped us to make the decision to
  purchase a mass spectrometer (LC-LTQ) and fold an
  existing Maldi-TOF into the nascent facility.

Our First LC-LTQ
Bin Deng, Manager
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Find Talented Staff
Dwight Matthews Co-Director
Bryan Ballif Co-Director
Bin Deng Manager
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Equip the Facility
Second LC-LTQ
LC-LTQ Orbitrap for High Mass Accuracy
Maldi-TOF
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Plan for Service From the Proteomics Wed Site
Guidelines for Facility Access, Sample
Submission, and Data Management Step 1 Initial
consultation Investigators should sign up for a
consultation prior to sample submission to ensure
a clear understanding of sample requirements for
processing through the facility. Sign up for a
consulation by booking a time here Consultation
Signups If you need help please contact Dr. Bin
Deng at 656-9722 or email to proteomics_at_uvm.edu.
Proteomics and Bioinformatics staff
participate! Step 2 Fill out the on-line sample
submission form and answer the questions listed.
Each sample must be accompanied by a completed
form. The information you provide helps to ensure
proper handling of your sample.Step 3 Only
trained persons directly operate mass
spectrometers in the facility. However, the users
are welcome to come, learn and participate in
their sample analysis. Proteomics Facility
Staff and Bioinformatics Core will provide data
analysis. It is best to send samples via FedEx
if you are a non-UVM user.
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• Next Steps 2006-2008
• Developing the User Base and Loyal Clientele
• Early Successes
• No Fees
• Seminars and Education Outreach to the Research
  Community
• Advertising and celebrating our successes
• Continuing Education of the Staff
• Surveys Under Construction
• Attract more outside clients

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Impact over 2 years 94 projects completed, 85 for
Vermont researchers and 9 for researchers outside
Vermont 32 projects were with COBRE faculty, 1
with the CCTS, 52 with INBRE faculty 9 papers
have been published in peer-reviewed journals (5
with COBRE faculty) Grant proposals using MS
data?? Yes! One recent R01 funded and also a
paper in Science for a COBRE investigator
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Satisfied Clients with new Publications
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PROTEOMICS OUTREACH
Bin Deng and Bryan Ballif
Janet Murray and Pat Reed
Two-D gels and mass spec analysis are being beta
tested at UVM before being taken to baccalaureate
institutions throughout the state.
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• Future Steps
• Business Plans to be Updated
• Personnel
• Equipment depreciation
• Next generation of equipment/services
• Consumables
• Overhead
• Plan for Sustaining this Facility

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Sustaining Facilities into the Future Getting
Started Facilitate with your VPR an
institution-wide over-view of existing
facilities Assess the impact of the existing
facilities on research competitiveness Have clear
measures of impact of the facility on the
institutions and regions research endeavor
Draw up business plans for each facility Review
what is available within the institution and
encourage the use of existing facilities rather
than recapitulating instrumentation through
faculty set up for an individuals lab.
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Review what is available in the region for
sharing of facilities and agreements on services
and pricing. Why start with regional?
In-person training ease of shipping samples
shared seminars and hands-on tutorials
Partner with other institutions so that a
university or state does not feel compelled to
build every possible facility. Decision about
which facilities to sustain on campus and long
term plan drawn up for sustaining and reviewing
this decision.
Find Synergies Thank you NERLSCD!! Regional
Facilities Database at www.uvm.edu/vgn
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• The JVH sustainablity plan would include
• Someone with an over-view of the facilities at
  the university and authority to coordinate the
  facilities into a working whole. Autonomous but
  collaborative.
• A policy to look toward outside sources first if
  the need for a technology arises decisions
  should be driven by data user base and impacts
• Brokered agreements so that faculty at the
  institution are given good prices and priority
  service if they must go outside for services
• For facilities at the institution, there should
  be yearly updated business plans that address the
  consumables, maintenance fees, staffing and
  depreciation of equipment
• Impacts should be reported yearly and an
  evaluation of the suite of cores and facilities
  on campus revisited periodically

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Most Important

• The institution should commit to supporting the
  staff salaries on base budget of the facilities
  to be sustained and recoup the other costs
  through fees for service.

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• Why support personnel?
• Talented personnel are key to the success of a
  facility.
• If the best technology cannot be made to work
  well and produce high quality outcomes it will
  not improve research competitiveness.
• It might even produce artifacts that will
  embarrass the researcher and institution.
• Leverage partner with other grant-funded
  infrastructure building programs and private
  sector.
• (NSF EPSCoR, DOE EPSCoR, and NASA EPSCoR are just
  three.)

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Thank you for your attention!