In this issue... 

1997 Santa Fe Highlights 
Patrinos Address 
Joint Genome Institute (JGI) Comes of Age 
JGI Sequencing 
JGI Informatics 
JGI and Bermuda Quality Sequence 
Grants Awarded for JGI Collaboration 
JGI Sequencing Clones 
Sequencing Strategies,Tools 
Gene-Discovery Resources 
Sequencing at NIH NHGRI 
Functional Genomics 
Data Surge Challenges Informaticists 
Genome Annotation: Informatics Advances Needed for Age of Functional Genomics 
ELSI: Rapid Progress Accelerates Societal Impact of Genome Research 
1999 DOE HGP Meeting Set for California 

Human Genome Project Administration 
New 5-Year Goals, Project Midpoint 
DOE, NIH Discuss Informatics 
JASON Group Review 
BER Genome Instrumentation Research 

In the News 
Private-Sector Sequencing Plan 
Bang for the Buck: Government-Backed Research Underpins Potentially High Payoff Ventures 
Palmisano Joins DOE OBER 
DNA Files series to be on NPR 
HUGO Addresses Sample Collection 
Sickle Cell Mice May Lead to New Treatments 
TIGR Sequencing 6 More Microbes 
Tuberculosis Microbe Sequenced 
C. Elegans Sequencing Nears Finish 
HGMIS Website Restructured 
cDNA Cloning Workshop Identifies Critical Issues 
Survey Identifies Growing Need for Synchrotron Analyses 
NCGR Announcements 

Publications 
Report on Functional Consequences of Gene Expression 
Book on Tuskegee Conference 
Book Focuses on Biomarker Implications, Conference Proceedings 
Genome Analysis Protocol Handbook 

Software and the Internet 
Mouse Genome Informatics Release 2.0 
New System Identifies Polymorphisms 
DOE Supports Web Site for 1997 AAAS Genome Symposium 
Expressed Human Genome Database 

Funding 
DOE ELSI 
NIH NHGRI 
NHGRI Initiates Mailing List 
U.S. Genome Research Funding 

Meeting Calendars & Acronyms 
Genome and Biotechnology Meetings 
Training Courses and Workshops 
Acronyms 

HGN archives and subscriptions   
HGP Information home 

JGI Informatics: Tracking a Moving Target

Providing informatics support for achieving "dream" targets of 100 Mb a year of Bermuda-quality sequence is an evolving process, said Tom Slezak, director of the JGI informatics team. "It can't happen in a single leap. It will ride a learning curve similar to all the other scientific and technological ones going on in parallel," he said. But a lag time for informatics support on these processes is inevitable because support requirements are not yet clear.

In general terms, informatics for sequencing encompasses clone resources and validation, sequence production, sequence analysis and annotation, informatics integration, and systems administration. Slezak gave an overview of various short-, medium-, and long-term solutions being implemented to meet these challenges.

Focusing on JGI's charter and scope, investigators are working toward jointly designing, developing, and deploying processes; and sharing hardware, software, expertise, and production goals. Prime areas of informatics concern include improving sequence quality-control tracking and reporting, increasing automation of finishing tasks, linking mapping data with sequencing, and starting some pilot informatics projects to support early functional genomics efforts. As to the last, Slezak cautioned, "We'd better get a head start on these, or we're going to end up with five different spreadsheets or other forms of information and a lot of duplication."

The JGI informatics team is using systems already in place at the three participating laboratories, sharing code, and standardizing where feasible. "The three sites will meet on the Web," Slezak said.

Medium-range goals (FY 1999-FY 2000) include adapting the most robust JGI shotgun system to scale up to 20 to 40 Mb per year. Major challenges are to modify process changes and automate sequence finishing. Slezak observed that large increases in automation present severe informatics challenges, such as moving from many small robots to automating individual processes to an automated factory. He also noted the difficulty of predicting how much these efforts will speed up finishing, and he warned that the system will hit inherent limits.

Turning to long-term plans, Slezak observed, "We can't scale up by bolting things together." A complete overhaul of the entire process --the biology, automation, informatics, perhaps even management-- will be needed, he said. One promising avenue for meeting long-term goals is participation by commercial and academic groups in developing some automation and laboratory information-management systems (see New Awards). Other long-term goals are to develop centralized databases, connect them with existing ones, and provide capabilities for Web-based navigation and display of all the data from any starting point.

The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v9n3).