Savio

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Singularity on Savio: containerized applications and mobility of computation

Singularity workflow, image credit: singularity.lbl.gov

Singularity is an emerging software tool that facilitates the movement of software applications and workflows between computational environments -- from a researcher’s laptop, to Berkeley’s high-performance computing cluster, Savio, to XSEDE’s national-scale clusters (e.g., Jetstream, Comet) or

ESPM postdoc crosses 150 years of observational biology with satellite data to mitigate biodiversity loss

Paul Elsen, postdoctoral scholar, UC Berkeley Department of Environmental Science, Policy, and Management

Graduating from UC Berkeley as a cognitive science major in 2006, conservation biologist Paul Elsen would have never guessed that he would return to Berkeley a decade later to become a postdoctoral scholar in the Department of Environmental Science, Policy, and Management. Following completion of his M.A. and Ph.D in Ecology and Evolutionary Biology at Princeton University, Elsen returned to the West Coast and is now a David H.

Digital Humanist aims to run OCR over a terabyte of rare book scans

Adam Anderson, Mellon Postdoctoral Fellow in the Digital Humanities

Since his college days at Brigham Young University (BYU), Adam Anderson has been measuring evenings and weekends in pages, rather than hours. “You can scan about 400 pages an hour, once you get in the groove,” he explains. Anderson, a Mellon Postdoctoral Fellow in Digital Humanities at UC Berkeley, has spent his career scanning texts in order to draw upon secondary literature in archaeology and computational linguistics.

Berkeley Research Computing celebrates 1,000 HPC users

Ted Xiao, BRC's 1000th user

On April 6th at 2:30 PM, Berkeley Research Computing (BRC) reached a new milestone: the 1000th user account created in the high performance computing (HPC) environment. The lucky recipient of the 1000th account was Ted Xiao, an M.S. student working with Prof. Claire Tomlin in the Electrical Engineering and Computer Science department.

Go from Analog to Digital Texts with OCR

An early modern text (English)

A collection of digitized texts marks the start of a research project —  or does it?

For many social sciences and humanities researchers, creating searchable, editable, and machine-readable digital texts out of heaps of paper in archival boxes or from books painstakingly sourced from overlooked corners of the library can be a tedious, time-consuming process.

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.

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