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InTheLoop | 03.24.2014

March 24, 2014

High-Speed Networks Democratize Science

For the first time, data collected and analyzed by a remote user of the National Center for Electron Microscopy (NCEM) has been analyzed and published. This accomplishment shows potential for the future of remote microscopy, and how high-speed networks like ESnet could democratize science. Most NCEM users—about 200 per year—currently travel to Berkeley Lab to conduct their experiments. But with the recent SWARPES accomplishment, NCEM staffers are optimistic about the future of remote microscopy for DOE-supported science. »Read more.

Students Learn About the Math of Images

Last week, seventh-grade students at Oakland's Head-Royce School got a special math lesson from Berkeley Lab's Daniela Ushizima. She connected their advanced linear algebra lessons to how images are processed and manipulated by computers, including popular apps many students use on their phones.
»Read more

Cray Blog Surveys Breadth of Edison's Science

NERSC's Richard Gerber was featured as a guest-blogger for Cray on March 20. His rundown of the largest science projects computing on Edison is an enlightening read, even for those who know a lot about what NERSC does. Cray welcomes guest contributors to their blog. Contact Jon Bashor with ideas. »Read more.

Memorial Service for Suzanne Stevenson

A public memorial service will be held for Suzanne Stevenson at 2pm, Saturday, March 29 at the El Cerrito Kingdom Hall, located at 532 Elm Street in El Cerrito. Suzanne, who died February 16, was working as an  administrative assistant at NERSC and had filled other roles with the Computing Sciences organization since 2006, starting out at CRD. El Cerrito Kingdom Hall is a three minute walk from the El Cerrito Plaza BART station. Parking is limited.

This Week's CS Seminars

The Open Microscopy Environment: Open Source Image Informatics for the Biological Sciences

Wednesday, March 26, 12pm -1pm | NERSC OSF, Room 238

Jason R. Swedlow, Centre for Gene Regulation & Expression University of Dundee, Dundee, Scotland, UK; and Glencoe Software, Inc. Seattle, WA, USA

Despite significant advances in cell and tissue imaging instrumentation and analysis algorithms, major informatics challenges remain unsolved: file formats are proprietary, facilities to store, analyze and query numerical data or analysis results are not routinely available, integration of new algorithms into proprietary packages is difficult at best, and standards for sharing image data and results are lacking. We have developed an open-source software framework to address these limitations called the Open Microscopy Environment (http://openmicroscopy.org). OME has three components—an open data model for biological imaging, standardized file formats and software libraries for data file conversion and software tools for image data management and analysis.

Performance-oriented Congestion Control

Thursday, March 27, 2014, 2pm - 3pm | Bldg. 50B, Room 1237 (NOC)

Mo Dong, Computer Science Department University of Illinois

More than two decades of research have shown that TCP's performance suffers in many environments. Efforts to improve its performance by providing rate feedback from network devices are hard to deploy. Numerous end host modifications of TCP address specific problems but fail to broadly improve performance across a range of challenging network conditions. Jumping out of the TCP family's architecture's deficiency, we propose Performance-oriented Congestion Control (PCC), a new congestion control architecture in which each sender selfishly controls its sending strategy based on empirically observed performance metrics. We show through large-scale experiments that PCC can significantly benefit multiple real-world applications with consistently improved performance across multiple challenging scenarios. Despite individual senders' selfish behavior, we prove that PCC converges to a fair equilibrium; moreover, experiments show even better fairness and stability than TCP. With PCC's significantly improved robustness and safety, we discuss different deployment scenarios of PCC and point out that PCC joins an evolving trend towards a better congestion control architecture.

Link of the Week: Shocked Physicist Learns His Big Bang Theory Is True

It's a surprisingly charming confluence of science and reality TV. A video that went viral this week shows physicist Andre Linde's reaction as he learned his theory about inflation in the early universe had been confirmed. Linde and his wife Renata Kallosh, both professors of physics at Stanford, can be forgiven if they react like winners of the Publisher's Clearinghouse Sweepstakes when a former post-doc delivers the news. This prize is priceless.  »Read more.