# Presentation: 486192

## BERAC Subcommittee Report on DOE-JGI Review

- November 16 – 18, 2005
- Walnut Creek, CA

## G6

**Wash U****	****	**
**Baylor****	****	**** ****	**
**Broad****	****	**** ****	**
**Venter****	****	****            **
**	**

**	****	****            **
***JGI******	*****	**

**What is Unique about the JGI Compared to other Sequencing Centers ?**

**G6**

**Biomed****	****	**
**Biomed****	****	****	**
**Biomed **
**Biomed****	**** ****	**
**Biomed +Non Biomed**
**User Facility, DOE Focus **

**Notes:**
Of 6 large genome centers emerging from the human genome project, JGI is the only one with exclusive non-biomedical focus and the only user facility, making sequence and analysis available for naïve and experienced scientists studying DOE-relevant problems. 

## 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