Building Technology Infrastructure and Sustaining It into the Future Judith Van Houten

1. 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

2. 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).

3. 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

4. First Step for VGN MicroarrayFacility: • 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.

5. 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

6. 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

7. 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.

8. 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

9. 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

10. Impact Grant Year 3 2007-08 Experimental design consultations with 16 investigators Completion of 27 microarray projects (292 GeneChips) Performed 93 RNA assessments: 59 PicoChips, 118 NanoChips, 3 small RNA’s chip (new service, implemented, August, 2008)

11. 2007-2008 Impact 2007-08 Publications (8) Grant Applications Trained graduate students, postdocs, techs Seminars & presentations (11) Support of Outreach Programs Assessment Quantitative Data Survey results

12. MICROARRAY OUTREACH Tim Hunter and Scott Tighe 2007-2008 Green Mt. College Marlboro College Norwich University Middlebury College Johnson State Castleton State Saint Michael’s 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!

13. 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

14. 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

15. 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

16. 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. Bin Deng, Manager Our First LC-LTQ

17. Find Talented Staff Dwight Matthews Co-Director Bryan Ballif Co-Director Bin Deng Manager

18. Equip the Facility Second LC-LTQ LC-LTQ Orbitrap for High Mass Accuracy Maldi-TOF

19. 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@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.

20. 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

21. 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

22. Satisfied Clients with new Publications

23. 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.

24. Future Steps • Business Plans to be Updated • Personnel • Equipment depreciation • Next generation of equipment/services • Consumables • Overhead • Plan for Sustaining this Facility

25. 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 institution’s and region’s 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 individual’s lab.

26. 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

27. 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

28. 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.

29. 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.)

30. Thank you for your attention!