The project to sequence the genomes of Phytophthora ramorum and Phytophthora sojae started in 2002. The sequencing of Phytophthora ramorum represented the fastest sequencing of a newly emerged pathogen other than the Severe Acute Respiratory Syndrome virus; Phytophthora ramorum was identified in 2000 and its draft sequence was complete by 2004. The work, which was…
Making Science’s Insights of the Decade list – twice
The December 17 issue of Science includes a special feature called “Insights of the Decade” and two of them feature work done by DOE JGI researchers. (Note: Free registration is required to read the articles online.) Genome research features prominently in Science’s Insights of the Decade list. (DNA helix image by DS from Flickr via…
Breaking the Petabit barrier, a Tweet at a time
Earlier this year, the DOE JGI teamed with the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory to scale up its computing infrastructure to meet increasing user needs and the rising amount of data being generated. ESnet traffic map by Jon Dugan, ESnet Network Engineering Group, LBNL On Dec. 14, the…
DOE JGI’s genomics data volumes on ESNet Updates
We observed for the first time significant volumes of genomics data traversing the network as the Joint Genome Institute sent over 1 petabyte of data to NERSC. JGI alone accounted for about 10% of last month’s traffic volume. Read more on ESNet.
Walnut Creek’s former city manager on the DOE JGI in the WalnutCreekPatch
“I recently had the opportunity to visit the Joint Genome facility [in the Shadelands]. It sort of flies under the radar. What was mind boggling was how the power of the equipment has multiplied so much in nine years. They said the problem they now have is managing the mountains of data they’re getting. They’re…
Unpredictable MDA biases in metagenomic analyses
Genomic studies of low-biomass environments is often limited by the amount of DNA available, and one solution has been to use a whole genome amplification technique that uses phi29 DNA polymerase known as multiple displacement amplification (MDA). When used in single cell genomic studies, one noted drawback of the procedure has been amplification bias that…
100 Rhizobium Genomes Project on INRA’s MyCorWeb page
A joint venture has been established between the Centre for Rhizobium Studies (CRS) led by Dr Wayne Reeve at Murdoch University (Australia) and the Joint Genome Institute (JGI, USA) led by the Head of the Microbial Program Dr Nikos Kyrpides to completely decipher the genetic code for 100 geographically distinct root nodule rhizobial strains.’ Read more on the…
DOE’s Magellan cloud project on ESnet
We were glad to see DOE’s Magellan project getting some well-deserved recognition by the HPCwire Readers’ and Editors’ Choice Award at SC10 in New Orleans. Magellan investigates how cloud computing can help DOE researchers to manage the massive (and increasing) amount of data they generate in scientific collaborations. Magellan is a joint research project at…
Iowa colleges team with DOE JGI to Interpret-A-Genome
Augustana and two other Quad-City higher education institutions—Eastern Iowa Community College District and Black Hawk Community College—have partnered together to adopt the microbe Meiothermus ruber and join the Interpret a Genome project through the U.S. Department of Energy-Joint Genome Institute (DOE-JGI). Read more at the Aledo Times Record.
Award for DOE’s Magellan Cloud Computing Project
One of the first key users of NERSC’s Magellan cloud computing system was DOE’s Joint Genome Institute (JGI). In March, the facility had a sudden need for increased computing resources, and in less than three days, NERSC and JGI staff provisioned and configured hundreds of processor cores on the Magellan system to match the computing…