WALNUT CREEK, CA—One of the challenges in making cellulosic biofuels commercially viable is to cost-effectively deconstruct plant material to liberate fermentable energy-rich sugars. The U.S. Department of Energy (DOE) is funding several projects focused on identifying enzymes in organisms that optimally degrade cellulosic feedstocks. One such source are fungi, which break down dead wood and…
Volvox carteri project on GenomeWeb
In this week’s issue of Science, research led by investigators at the Department of Energy’s Joint Genome Institute examines the organismal complexity of the multicellular green alga Volvox carteri. Simon Prochnik et al. sequenced the Volvox genome to 11.1-fold coverage using a whole-genome shotgun approach; when compared to Chlamydomonas reinhardtii, its unicellular relative, the team…
Genome Signatures Enable Tracking of Algal Complexity
WALNUT CREEK, CA—On the long and difficult road toward a carbon-neutral source of transportation fuels, the U.S. Department of Energy (DOE) is pursuing a diversified approach. This effort involves exploring a range of potential new fuel sources in nature: from plants that may serve as cellulosic feedstocks—fast-growing trees and perennial grasses on land—to oil-producing organisms…
Volvox genome belies “Small is Simple” Axiom
In the July 9, 2010 issue of Science, researchers led by the DOE JGI and the Salk Institute report on the 138 million-base genome of the multicellular alga Volvox carteri. The work complements the genome of the unicellular alga Chlamydomonas reinhardtii, which was sequenced by the DOE JGI in 2007 and is used by researchers…
DOE JGI’s role in managing Human Microbiome Project data on redOrbit
At JGI, Kyrpides oversees projects such as GenePRIMP, a highly rated quality control program for genome sequencing, and GOLD, the Genomes On-Line Database. GenePRIMP stands for “Gene PRediction IMprovement Pipeline, and it consists of a series of computational units that can be used to significantly improve the overall quality of the predicted genes in any…
DOE JGI’s role in managing Human Microbiome Project data on Medical News
“The HMP project catalog is a unique worldwide resource,” says molecular biologist Nikos Kyrpides of Berkeley Lab’s Genomics Division, who heads the Genome Biology and Metagenomics Programs for the Joint Genome Institute (JGI) and is the co-principal investigator of the DACC. “It has a central role in the HMP, not only in maintaining the list…
Characterizes/Publishes Anti-Reservoir-Souring Microbe
Reservoir souring, the production of hydrogen sulfide in oil wells as a result of downhole activity by a specialized group of microorganisms called sulfate-reducing bacteria (SRB), is a detrimental process of great concern to the oil industry. As petroleum reserves age and water injection is implemented for pressure maintenance, there is an inherent risk of…
DOE JGI’s role in managing Human Microbiome Project data
At JGI, Kyrpides oversees projects such as GenePRIMP, a highly rated quality control program for genome sequencing, and GOLD, the Genomes On-Line Database. GenePRIMP stands for “Gene PRediction IMprovement Pipeline, and it consists of a series of computational units that can be used to significantly improve the overall quality of the predicted genes in any…
DOE JGI’s use of Isilon scale-out NAS on EarthTimes
Leveraging Isilon’s X-Series, featuring its OneFS® operating system, JGI has unified 25 genome sequencers onto a single, high performance, highly scalable, shared pool of storage, reducing storage management. The JGI is also using the Isilon IQ 5000S-SSD, which combines SAS and Solid State Disk (SSD) drives as an additional storage resource for its team. With…
DOE JGI’s use of Isilon scale-out NAS on San Diego, CA’s CBS 8
Prior to deploying Isilon scale-out NAS, the JGI used more than six network file system (NFS) servers to power its 25 DNA sequencers. As the JGI’s genomic sequencing operations expanded, its NFS servers were unable to scale in-line with demand, fragmenting data across its separate file systems and limiting the performance of both the JGI’s…