86. JGI Informatics and the PSF Network 

Tom Slezak, Mark Wagner, Lisa Corsetti, Sam Pitluck, Arthur Kobayashi, Mimi Yeh, Brian Yumae, and Peg Folta 
Joint Genome Institute; Lawrence Livermore National Laboratory, Livermore, California and Lawrence Berkeley National Laboratory, Berkeley, California 
slezak@llnl.gov 

The component labs of the JGI sometimes appear to have little more than their funding source in common, both in biology and informatics. Meeting the stiff FY98 production goals was more of a miracle of elasticity of existing systems and people than any sort of fusion of component parts or philosophies. It is only now that we are actually working together in the PSF that we are being truly compelled to develop a new common culture. In some senses, informatics is being used as both the carrot and stick with which to overcome many of the differences, gratuitous or not, that have evolved at the JGI member labs. 

Consolidation in informatics can only occur if there is corresponding consolidation or similarity in the underlying biological methods. Systems developed for transposon-based sequencing are highly dissimilar from those developed for shotgun strategies. Similar differences occur in mapping systems, which in the JGI have ranged from Claris Draw to Sybase. It is not feasible to make dramatic changes to processes that are under extreme production pressures; we are challenged to provide gradual, seductive improvements that bring about unification without derailing production ramps. 

The long-term vision for JGI informatics is that information should be available in a JGI-centric view throughout the entire process: from mapping (via several methods), to production sequencing (allowing for multiple methods), to annotation and submission (allowing for several styles of manual and semi-automated annotation), and eventually to a range of functional genomics and structural biology. We are in the very earliest days of implementing this dream, as we struggle with production ramp rates unmatched anywhere that demand full effort from our best people who would otherwise be building our new systems. We will discuss our early efforts and our aspirations for this important first year of true "Joint-ness". 

The PSF network has been designed to accommodate growth and flexibility in light of uncertain future demands. It features a cable plan that allows any jack to be a network, digital voice, or analog fax line as needed. The network is segmented into a high-reliability subnet for DNA sequencer data acquisition and primary server/storage functions, and another subnet for office and lab computers. We acknowledge the excellent work and contributions of the LBNL Communications (Sig Rogers), LBLnet (Ted Sopher), and ESnet (Jim Leighton) staffs in making the PSF network happen on time and on budget. 

This work was performed by Lawrence Livermore National Laboratory under the auspices of the U.S. Department of Energy, Contract No. W-7405-Eng-48.