Savio

BRC Supports Biostatisticians in Effort to Develop Software for Traumatic Injury Treatment and Outcome Predictions

Alan Hubbard and research group colleagues, Jan 2017

What do the Phanerozoic eon and Precision Medicine have in common? For one thing: the statistical analyses of Alan Hubbard, UC Berkeley Associate Professor of Biostatistics, and head of the Division of Biostatistics at the School of Public Health.

IPython notebook available to ease data transfer between Savio and Box

Screenshot from the iPython notebook configured for Box access,TransferFilesFromBoxToSavioScratch.ipynb

For researchers running computation on the Savio high-performance compute cluster, data transfer can be a challenge. A new IPython notebook simplifies data transfer from the free Box collaboration platform to a Savio user’s scratch folder, and provides a template for users to develop their own algorithms that analyze data stored in Box.

Savio supports Doudna Lab biophysicist’s investigation of human protein production

Stephen Floor

“I have always believed in following the science,” says Stephen Floor, a postdoctoral researcher in the Doudna Lab, led by UC Berkeley Professor of Biochemistry, Biophysics, and Structural Biology, Jennifer Doudna. Floor’s self-described “circuitous” academic journey has taken him from computer science, to physics, and now, to molecular biology.

Steve Masover's picture

Savio capacity expands through faculty contributions

Galileo supercomputer wiring

Faculty contributions drove this year’s increase in computational capacity on Savio, the Berkeley Research Computing (BRC) Program’s shared High Performance Computing (HPC) cluster. Condo contributions, including those expected to be added by the end of the year, totaled 63 nodes and 1,368 cores: a capacity expansion of approximately 19%, valued at about $400,000.

Atmospheric chemists use Savio to build computational gas emission models

Professor Ron Cohen and team

Ron Cohen, Professor of Chemistry and Earth and Planetary Sciences at UC Berkeley, and graduate students Alexis Shusterman, Josh Laughner, and visiting Harvard graduate student Alex Turner, are “trying to create a model of the world that matches the observations of the world.” That is, Cohen’s team is using sensor technology to measure the concentrations of atmospheric gases at both local and global scales, and from that data develop computational models that describe the emission processes and rates that cause those observations.

Aron D. Roberts's picture

Savio HPC cluster intermediate training on September 27, 2016

Savio training, 2 Aug 2016, AIS

An intermediate-level training session on the use of Savio and other Berkeley Research Computing high performance computing (HPC) clusters (Cortex and Vector) will be offered on Tuesday, September 27, 2016. If you’re a current or prospective user of one of these clusters, and already have some experience using HPC resources, you are invited to expand your skills via this free training.

Epidemiologists develop a computational tool to optimize study design

Screenshot, StudySimulator.com

Professor Jennifer Ahern of the School of Public Health, and two staff researchers, Masters of Public Health (MPH) Ellie Matthay and Scott Zimmerman, are developing a software tool called the Study Simulator, a web-based simulation generator that will allow investigators to identify optimal study designs and methods of analysis for research inquiries in Public Health and Epidemiology.

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