Using desktop computers, ORNL is preparing to establish a scientific "bookkeeping operation for bioenergy". Ed Uberbacher, who leads the Genome Analysis and Systems Modeling Group of ORNL's Biosciences Division, says that Oak Ridge researchers have the experience to keep track of data, experimental equipment and chemicals by using Nautilus™ a software system produced by Thermo Electron Corp. for managing, sharing and protecting laboratory information.
"We developed database technologies for DOE's Shewanella Foundation to allow researchers investigating Shewanella oneidensis bacteria to share data and compare the sequences of genomes of bacteria that respond differently to toxic metals in their environment," Uberbacher says. In this way, researchers might be able to identify networks of genes and proteins that destroy contaminants.
To build a bioinformatics infrastructure for bioenergy research, Uberbacher's GASM group is working with Igor Jouline of the University of Tennessee and former ORNL researcher Ying Xu and Bob Scott, both of the University of Georgia. The researchers have broad expertise in developing models of microbial gene regulatory systems.
The research is structured to enable partner investigators to work together on experiments and share and compare data they generate using different instruments and reagents at different sites. The experiments to advance bioenergy will use a variety of tools, such as electron microscopes, fluorescent microscopes, microarrays, mass spectrometers and computers. Each information system must track biochemical assays, image data sets, expression microarrays and mass spectra.
Researchers in the GASM Group and ORNL's Computer Science and Mathematics Division established a Laboratory Information Management System for DOE's Genomics: GTL Center for Molecular and Cellular Systems involving researchers at ORNL and Pacific Northwest National Laboratory. The system helps researchers identify and characterize proteins in Rhodopseudomonas palustris, a bacterium that can produce hydrogen depending upon how it is grown. Researchers are growing R. pal microbes in different ways with special tags, extracting their protein complexes, identifying and characterizing the protein complexes using mass spectrometers and imaging tools, and sending mass spectra and other data to computational biologists for interpretation. The researchers, who decode the interactions of 16 target proteins per week, are trying to determine which protein complexes in R. pal produce hydrogen or carry out some other function of interest to DOE. The center promises to characterize these protein groups for other microbes of interest to DOE and outside collaborators. ORNL has provided internal funding to develop data exchanges and networks for ethanologens, microbes that ferment sugar to alcohol.
"The Laboratory Information Management System provides a model on how to undertake a huge bookkeeping job for a host of partners, somewhat like what Wal-Mart does to keep track of inventory at all its stores," Uberbacher says. "The job is not glamorous, but it is essential to the accuracy of every project's research results to keep track of each piece of the avalanche of data associated with all the experiments." —Carolyn Krause
Web site provided by Oak Ridge National Laboratory's Communications and External Relations