Berkeley Lab

Biosciences Area

JGI Part of Berkeley Lab Team Receiving HPCwire Award in Life Sciences

At SC21, the HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project. The award recognized the release of MetaHipMer, an end-to-end genome assembler that supports “an unprecendented assembly of environmental microbiomes. 

“They produced fantastic scientific results this year by assembling a collection of large datasets that will enable scientists to explore and collect data in new ways,” said JGI Chief Informatics Officer Kjiersten Fagnan of the award. “We’re excited to be able to offer this capability to the JGI user community moving forward and to assemble, for the first time these large environmental microbial data sets for JGI users, which include projects looking at wildfire impacts, carbon cycling, and the microbial dynamics in freshwater lakes over a several year period.”  

A Community-driven Data Science System to Advance Microbiome Research

The National Microbiome Data Collaborative will develop an open-access framework for harnessing microbiome data to accelerate discoveries

The National Microbiome Data Collaborative (NMDC), a new initiative aimed at empowering microbiome research, is gearing up its pilot phase after receiving $10 million of funding from the U.S. Department of Energy (DOE) Office of Science. Led by Lawrence Berkeley National Laboratory (Berkeley Lab), in partnership with Los Alamos (LANL), Oak Ridge (ORNL), and Pacific Northwest (PNNL) National Laboratories, the NMDC will leverage DOE’s existing data-science resources and high-performance computing systems to develop a framework that facilitates more efficient use of microbiome data for applications in energy, environment, health, and agriculture.

JGI’s CIO Part of Winning SC18 Team

On November 15, 2018, at the International Conference for High Performance Computing, Networking, Storage and Analysis (SC18) Conference, teams led by Lawrence Berkeley National Laboratory (Berkeley Lab) and Oak Ridge National Laboratory (ORNL), respectively, shared the 2018 ACM Gordon Bell Prize.

Congratulations to JGI’s Chief Informatics Officer Kjiersten Fagnan, who was part of the ORNL-led, seven-member team. The 12-member Berkeley Lab team was recognized for training a deep neural network to identify extreme weather patterns from high-resolution climate simulations using high-performance computers.

Read the full story on the JGI website.

Computing Sciences and Biosciences Hold Machine Learning Workshop

The Lab’s Computing Sciences and Biosciences Areas jointly held a week-long workshop focused on machine learning in data science, the goal of which was to build bridges through a common foundation in statistical computing. Thirty attendees from Biosciences, Computing Sciences, and Lab IT received hands-on training provided by Data Incubator before engaging in a “hackathon” to apply the techniques to relevant science problems and data sets.

DOE User Facilities Join Forces to Tackle Biology’s Big Data

Six proposals have been selected to participate in a new partnership between two DOE user facilities at Lawrence Berkeley National Laboratory through the FICUS initiative. The expertise and capabilities available at JGI and NERSC will help researchers explore the wealth of genomic and metagenomic data generated worldwide through access to supercomputing resources and computational science experts to accelerate discoveries. Read more on the DOE JGI website.

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