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BERAC Subcommittee Report on DOE-JGI Review

BERAC Subcommittee Report on DOE-JGI Review. November 16 – 18, 2005 Walnut Creek, CA. What is Unique about the JGI Compared to other Sequencing Centers ?. Sanger (UK) Wash U Baylor Broad Venter. Biomed Biomed Biomed Biomed Biomed +Non Biomed User Facility, DOE Focus. G6.

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BERAC Subcommittee Report on DOE-JGI Review

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  1. BERAC Subcommittee Report on DOE-JGI Review November 16 – 18, 2005 Walnut Creek, CA

  2. What is Unique about the JGI Compared to other Sequencing Centers ? Sanger (UK) Wash U Baylor Broad Venter Biomed Biomed Biomed Biomed Biomed +Non Biomed User Facility, DOE Focus G6 JGI

  3. Production Genomics Facility (PGF) 250 FTE’s: 1/2 LBNL, 1/2 LLNL 105 DNA sequencers running 24/7/365 Annual capacity 30 billion basepairs >100 user projects initiated annually JGI Partnership 5 partner labs (LBL, LLNL,LANL, ORNL, PNNL) Distributed tasks Microbial finishing, annotation, project management Efforts coordinated by JGI Director JGI Fact Sheet

  4. BERAC Subcommittee for Review of DOE-JGI • Mel Simon (chair) California Institute of Technology • Jim Tiedje, MSU • Bruce Birren, Broad Inst., MIT • Klaus Berkner, LBNL (Ret.) • Bruce Chrisman, Fermilab, IL • Linda Horton, ORNL • Richard Mural, Windber Inst, PA • Jane Rogers, Sanger Ctr, Hinxton, UK • Richard Wilson, Washington U, St. Louis • DOE Staff: Dan Drell, Kent Lohman • NHGRI observer: Jane Peterson

  5. Subcommittee Findings • In the area of Science, the committee was delighted to find that with respect to scientific vision, JGI was doing very well in: • implementation of its role as a national user-facility and, • focusing on DOE mission objectives. • Furthermore, the PGF operates at the state of the art with respect to cost, quality, and quantity of sequences that it produces

  6. Subcommittee Findings • In short, the committee felt that the JGI represents a: • major asset in the DOE’s portfolio. • is engaged in first-rate science. • has focused on a niche where sequencing contributes to both pioneering basic science and to the specific missions of the DOE - energy, carbon sequestration and bioremediation. • Was highly impressed with the senior management team and with the operations staff and middle management.

  7. Subcommittee Recommendations • A new MOU between LLNL/LBNL clarifying roles and responsibilities relative to procedures, especially regarding safety and cyber security, should be given high priority. • The JGI directors should review the organizational structure of the JGI to establish clear lines of authority and responsibility

  8. Subcommittee Recommendations • The JGI should develop plans to implement a scalable process for assembly of large genomes. • The JGI should further develop plans to: • i) reduce the time lag between the release of genome assemblies and annotations; • ii) scale-up genome annotation activities; • iii) extend the capabilities of the system in an ongoing fashion; and, • iv) increase the transparency of the annotation process both to the Walnut Creek staff to improve their ability to manage it and to the wider user community.

  9. Subcommittee Recommendations • It is imperative that a new MOU clarify the safety responsibilities of the two laboratories and that unambiguous guidelines be established for PGF employees. • Establish a system such that the JGI Director can get timely information on recordable and lost-time injury rates. Use standard definitions for TRC and DART.

  10. Subcommittee Recommendations • Consider using the same review committee for all or part of the reviews (to ensure uniformity), and organize parallel coordinated calls. • Improve the demographics of the CSP proposal review committee. Having a large number of UC “winners” coupled with a proposal review committee dominated by UC staff could bring the independence of the review system into question.

  11. Subcommittee Recommendations • Get input from the users on the peer review process and implement suggestions for improvement. Also, seek advice from other advisory groups • Distribute the user survey on at least an annual basis, and also at completion of project.

  12. Subcommittee Recommendations • Expand the use of project management techniques and systems and appropriate staff training in the use of formal project management. • Establisha routine (monthly or quarterly) meeting between the JGI Head of Operations and his/her LBNL counterparts. • Develop a plan for covering senior level vacancies while replacement hiring is undertaken

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