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

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

Advancing Science with DNA Sequence JGI Fact Sheet 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

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

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

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.

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

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.

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.

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.

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.

Subcommittee Recommendations Expand the use of project management techniques and systems and appropriate staff training in the use of formal project management. Establish a 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