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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… [Read More]

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… [Read More]

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… [Read More]

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… [Read More]

DOE JGI’s use of Isilon scale-out NAS on redOrbit

By unifying its DNA sequencing operations onto 2PB of the Isilon IQ 72000X, the JGI has centralized data access. With its leading-edge, highly data-intensive R&D work powered by a separate, Isilon IQ 5000S-SSD cluster, the JGI’s DNA sequencing operations have a unified and dedicated storage resource, eliminating data fragmentation and performance bottlenecks to help speed… [Read More]

DOE JGI’s use of Isilon scale-out NAS on PRNewswire

“The JGI’s research is critical to reducing our nation’s dependency on foreign oil and replacing it with new, cleaner and more efficient energy resources,” said Sam Grocott, vice president of marketing, Isilon Systems. “This research exemplifies the term ‘mission-critical,’ requiring a storage solution with the highest levels of scalability, performance and reliability to ensure it… [Read More]

Frog genome project on BBC

“When human genome work was wrapping up around 2002, we were discussing what should be next,” JGI’s Uffe Hellsten told BBC News. “At that time there were a couple of furry mammals in the pipeline, and the chicken and at least two fish – but there seemed to be a gaping hole in the branch… [Read More]

GenePRIMP QC tool on Genetic Engineering & Biotechnology News

The program, said Pati, identifies gene-calling errors such as potentially incorrect gene start and end positions, large overlaps between genes, fragmented genes and missed genes. Gene-calling errors, noted Pati, can range from two percent to as much as 30 percent of the original genes identified in the genome and are dependent on many factors, such… [Read More]

GenePRIMP QC tool on PhysOrg

“There are a lot of different tools used for predicting genes in prokaryotes,” Kyrpides said. “The major problem we have is that they all produce very variable results. This impedes our ability to compare genomes sequenced and annotated from various sources, as they use different tools for gene prediction. GenePRIMP is not substituting any of… [Read More]