Friday, May 29, 2009

Of Pomegranate Juice and Longevity (and PLOS Genetics)

Bioengineering professor Trey Ideker is the senior author on a paper out today in PLOS Genetics that provides an explanation for the seemingly paradoxical finding that small exposure to oxidative conditions may actually offer protection from acute doses. (Full press release here, written by Debra Kain from the UC San Diego School of Medicine).

Remember that oxidative stress has been linked to aging, cancer and other diseases in humans.
“We may drink pomegranate juice to protect our bodies from so-called ‘free radicals’ or look at restricting calorie intake to extend our lifespan,” said Trey Ideker, PhD, professor of bioengineering at the Jacobs School of Engineering and chief of the Division of Genetics in the Department of Medicine at UC San Diego’s School of Medicine. “But our study suggests why humans may actually be able to
prolong the aging process by regularly exposing our bodies to minimal amounts of

The paper is published in an open access journal (PLOS Genetics), so anyone can go directly to the paper and dig in (be sure to enjoy figure 3, which I find quite pleasing to look at.)
The first author is Ryan Kelley, who completed the Bioinformatics program at UC San Diego and is now working at Illumina.

CMRR Students Selected as Young Marconi Scholars

CMRR graduate student Eitan Yaakobi (in photo above) and CMRR visiting graduate student Marco Papaleo have been selected as Marconi Scholars for 2009 by the Marconi Society. The honor includes a $4,000 cash prize, which will be presented at the Marconi Society Award Dinner in Bologna, Italy, on October 9, 2009.

Eitan Yaakobi received his B.A. and M.Sc. degrees from the Technion - Israel Institute of Technology, Haifa, Israel, in 2005 and 2007, respectively, from the Computer Science Department. He is currently a Ph.D. candidate in Electrical and Computer Engineering at the University of California, San Diego, where he is associated with the Center for Magnetic Recording Research (CMRR). His advisors are Professor Paul Siegel, Professor Jack Wolf and Professor Alexander Vardy. His research interests include algebraic error-correction coding, coding theory, and their applications for digital data storage, and in particular for flash memories.

According to Yaakobi's reserach profile:
"Flash memories are, by far, the most important type of nonvolatile computer memory in use today. They are employed widely in mobile, embedded, and
mass-storage applications, and the growth in this sector continues at a
staggering pace. In this research we mainly focus on coding for flash memories
in order to improve the reliability, capacity and endurance of the memory."

Marco Papaleo is a visiting graduate student under Professor Paul H. Siegel and Professor Jack K. Wolf. He received his B.S. and M.Sc. degrees (summa cum laude) in telecommunication engineering from the University of Bologna, Italy, in 2003 and in 2006, respectively. He received an award for one of the three best theses in telecommunication engineering from University of Bologna for the academic year 2004-2005. In January 2006, he joined the Advanced Research Center on Electronic Systems for Information and Communications Technologies "Ercole De Castro" (ARCES) at the University of Bologna, where he also began his Ph.D. studies in 2007. In the summer of 2008 he was a visiting Ph.D. student at the German Aerospace Center (DLR) Institute of Communications and Navigation in Wessling. He was involved in the design and analysis of LDPC convolutional codes. In 2006, he was a visiting affiliate student at the University College of London (UCL), in England. His current research activities are focused on the next generation wireless telecommunication systems, for both terrestrial and satellite networks. In particular, he is interested in the design and performance
evaluation of error control coding (with emphasis on packet level coding).

Got a moment? Check out the CMRR Winter 2009 Report here.

(The Marconi prize also includes $1,000 to help defray travel expenses to the event in Bologna, Italy...hopefully some of that money can be used for buying food in Bologna...which is a stand-out food destination, even in Italy, where almost all the food is good.)

Thursday, May 28, 2009

Bioinformatics and Systems Biology Student publications

(above: Nitin Gupta is a PhD student in bioinformatics at UC San Diego)

From Shankar Subramaniam, Chair of the Dept of Bioengineering and director of UC San Diego's Bioinformatics program.
We are witnessing the birth of a new era in biology. The ability to decipher the genetic code of living organisms is dramatically changing our understanding of the natural world and promises to substantially improve the quality of human life.

The new bioinformatics and systems biology site went live earlier this year. I especailly like the student publiations page because it pulls together many of the new papers from graduate students who are in different departments but are all working in the ares of bioinformatics.

Wednesday, May 27, 2009

Underwater Sensor Update

Yesterday, I posted a press release about Bridget Benson, the computer science PhD student who is building energy efficient underwater sensor networks that are badly needed by scientists who study watery environments. She is also the SoCal volunteer coordinator for Reef Check, a nonprofit that includes volunteer divers in their surveys of the Southern California coast.
Reef Check has a survey this Saturday in La Jolla Cove. But it looks like Bridget won't be there. Instead, she will run the survey the following weekend up in Palos Verdes, off the coast of Los Angeles.
I posted a photo from the Reef Check photo gallery showing Bridget Benson in her dive gear. Photo credit: Reef Check.

Tuesday, May 26, 2009

Underwater Sensor Nets: Sonar on the Cheap...sort of

Ever since (and I'm well sure before) the days of sending messages in bottles across the sea, it has been hard to get information to travel through the water. Sure, there are the expensive sonar systems that the Navy uses. But researchers collecting data on coral reefs or kelp beds don't have that kind of budget. A group of information technology pioneers at UC San Diego led by computer science PhD student Bridget Benson are well on their way to a new breed of cheap, reliable nets of underwater sensors for environmental monitoring. Yesterday, computer science professor Ryan Kastner presented some of the teams latest work on figuring out which hardward platforms are the least energy consuming at an IEEE workshop in Rome.

Back here in San Deigo, Bridget Benson, the PhD student leading the project, has an interesting perspective: can see the challenge from two sides, literally. In her spare time, Bridget works as a volunteer coordinator for the nonprofit group Reef Check. In this role, she gets experienced divers to help Reef Check monitor the California coastline. This is the kind of project that nets of underwater sensors could someday help with.

Learn more about Reef Check here. Their next dive in La Jolla cove is this Saturday, May 30.

Electrical engineering undergrad Brian Faunce is the person in the lowest photo of the bunch above.
“In class, you learn a lot of theory, but you don’t learn how to revise a schematic, layout the printed circuit board, assemble the circuit and then perform field tests. I have friends at other schools, and when it comes to internships and projects, they are just not available at other schools the way they are here,” said Faunce.

Wednesday, May 20, 2009

Student Life = Entrepreneur Life

UC San Diego are taking their career prospects into their own hands...literally. They are commercializing technologies, starting companies, and generally making futures for themselves and for many more people. One of the central events to the entrepreneurial culture that has grown strong over the past few years is the UC San Diego Entrepreneur Challenge.

More info below on the June 1, 2009 event:

Students at the University of California, San Diego will be vying for $80,000 in prizes that will be awarded on June 1st at the culminating event of the 3rd Annual UC San Diego Entrepreneur Challenge Business Plan Competition. The event, open to the public, will take place at the Lawrence Family Jewish Community Center in La Jolla from 6-8pm and will host the premier gathering of entrepreneurs, scientists, engineers, business professionals, and students from throughout the San Diego area. Five teams that have been selected from over 70 that entered the competition at the beginning of the academic year will have the opportunity to pitch their businesses to an all star panel of live judges including Rady School and SDSU business school deans Bob Sullivan and Gail Naughton, CONNECT CEO Duane Roth, President of the Foundation for Enterprise Development Mary Ann Beyster, and powerhouse investors Larry Bock and Leo Spiegel. The top three teams will be awarded a total of $40,000 in unrestricted cash prizes as well as $30,000 in services awarded by DLA Piper, a world class leading legal firm specializing in intellectual property and early phase start-ups. The remaining $10,000 cash will be divided to the winners of the competition’s subcategories: IT/High Tech, Biotech/Life Sciences, Social Entrepreneurship, Clean Tech, and a dedicated category for undergraduate participants. RSVP is required. RSVP at

Dany Kitishian
CEO, UC San Diego Entrepreneur Challenge
(318) 278 7555

trying out twitter

I just started up a twitter account: UCSDJacobs

Time will tell how tweeting from the Jacobs School press office first update said that I was watching the Junkyard Derby video I made last week. And it's true, I was watching it again because I was exporting a higher resolution version for my colleagues over at CAP (the Corporate Affiliates Program) who are going to show it at the next CAP board meeting.

Tuesday, May 19, 2009

Electrical engineering and computer science undergrads in ACM TechNews

Congrats to the robotic mouse makers at the Jacobs School. They landed in the 18 May issue of ACM TechNews. (In the photo above, they are cutting their own metal pegs for the maze). The 4 minute video is here, if you haven't seen it already.

The RSS feed for ACM TechNews is here...and I also added it to my new list of tech sites at the bottom of the right-side column of this blog.

Robotic Mouse Makes Maze Debut at UC San Diego Jacobs School of Engineering

University of California, San Diego (UCSD) Jacobs School of Engineering researchers have designed and built a robotic mouse and developed software to teach the robot to navigate through a maze. The robot navigates the maze using a pair of wheels and two self-lubricating sliders made from high-tech cutting board material. The robot, which is about the size of a cylindrical cookie jar, uses a set of distance sensors that project light onto the maze walls, which bounces back and is used to identify openings. The sensor-based approach gives the robot vision capabilities without having to deal with the complexities surrounding cameras, says UCSD student Jeffrey Wurzbach, who worked on the project. The robot was built for the MicroMouse competition, which tasks students with controlling an entire robotics system, including hardware, low-level code, high-level code, and all related debugging tools. UCSD professor Charles Tu says graduate school admissions committees and potential employers are looking for this kind of experience. In addition to designing and building the robot, the team spent five weeks building the 10-foot by 10-foot maze for the competition.

From "Robotic Mouse Makes Maze Debut at UC San Diego Jacobs School of Engineering"

Friday, May 15, 2009

Bohemian Rhapsody Song Segmentation

Bohemian Rhapsody is a heterogeneous song. We know that. Now, computers can "know" it too. I am still talking about the research in the press release I put out yesterday. This is a photo showing the new song segmentation process in action, for Queen's Bohemian Rhapsody.

Also, I'm liking to 2:30 second video about the making of the Facebook music discovery game video...again.

Chris Jablonski from ZDNet and sister sites blogged about the music dicovery Facebook games and video.

Thursday, May 14, 2009

Tuesday, May 12, 2009

Junkyard Derby Video 2009

Pirates AND "space pirates from space" competing in the same UC San Diego student competition. That's right...and there is so much more to Junkyard Derby, a student event in which students build cars from junk and then race them down a hill on campus.

Congratulations to the AIAA team, which won first place. The silver shuttle/plane-like car was driven by Colin Sheredy, an undergrad from the mechanical and aerospace engineering department.

There are photos below and on the Calit2 photostream.

Friday, May 8, 2009

Technology for Early-Cancer Diagnosis Leads Bioengineering Grad Student to Many Prizes and a Startup Company

Raj Krishnan is a bioengineering graduate student leading a research project that may change the way cancer is diagnosed. His goal is to create new tools that catch cancer at its very earliest stages by identifying secondary biomarkers that are present long before tumors appear or other biomakers are evident.
In 2009, Krishnan has won three major University of California awards for his research. He is also heading up a startup company that aims to make this technology available to the world, where it may help people catch cancer earlier...and when it comes to cancer diagnsis, earlier is certainly better.

Tuesday, May 5, 2009

Robotic Mice in a Maze

A couple of Fridays ago, I spent the afternoon with five of the Jacobs School undergrads who make up the UC San Diego MicroMouse team. They were deep into prep mode because the following morning, their robotic mouse had to be ready to solve a maze with no help from humans.

Of course there were midterms to be preparing for, and all the usual Friday afternoon distractions on a college campus, but none of that mattered. Software bugs had to be found and fixed. The maze had to be cleaned. And there was even another algorithm to be implemented.

If you have five minutes, watch the video embedded below [high rez YouTube version here] (or read the full story). I hope it gives you a glimpse of team engineering in action.

The students made the sofa in the background from the recycled wood from the deck they built as a level construction platform for the maze.

The fireworks (above) started when students cut nails for the maze.

Monday, May 4, 2009

Junkyard Derby is this Week!

Jacobs School engineering students will transform junk into racecars this week at UC San Diego. The three-day marathon starts on Wednesday afternoon with the kick-off BBQ and junk-dash. It's a lot of fun to watch students diving into a pile of junk in search of that perfect racecar part. Grocery carts are always appealing...though I don't know how well the actually work in the end.

After two nights of furious building, the students race their junk cars down Peterson Hill, near the UC San Diego library.
Junkyard Derby 2009 Schedule:

Wednesday, May 6
Kickoff Event and BBQ :: 5-6pm
Build Time :: Junkyard open from 7pm-2am

Thursday, May 7
Build Day :: Junkyard open from 8am-2am

Friday, May 8
Race Day :: 10:30am-3pm at Peterson Hill
Junkyard Derby is a great event run by TESC (Triton Engineering Student Council) at UC San Diego's Jacobs School of Engineering

Sunday, May 3, 2009

Surf's Up: Physics of Surfing

photo credit: Sean Masterson / For The Times

"A break from classes to learn how waves break."

That's the headline for a Los Angeles Times story by Tony Perry on the Physics of Surfing freshman seminar co-taught by Stefan Llewellyn Smith, a professor of mechanical and aerospace engineering from the Jacobs School and David Sandwell, professor of geophysics at UC San Diego's Scripps Institution of Oceanography.

Here is a story and video about the physics of surfing class from UC San Diego written by Ioana Patringenaru.

Friday, May 1, 2009

ABC = Amazon Belongie Connection

At least, that's one way to look at it. Earlier this week, Amazon Web Services LLC (AWS), a subsidiary of, Inc Amazon announced "AWS in Education," a set of programs that enable the academic community to easily leverage the benefits of Amazon Web Services for teaching and research.

Here is a quote from computer science professor Serge Belongie from the UC San Diego Jacobs School of Engineering.

“The grant we have received from the AWS in Education program will dramatically increase the reach of my student group's collaboration with the National Federation of the Blind (NFB) to develop distributed assistive computer vision technology for the visually impaired,” said Serge Belongie, Associate Professor at the University of California in San Diego.

Read more about this vision technology here.