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  • CSE Faculty Affiliate Honored with Vilcek Prize

    CSE faculty-affiliate Rob Knight is a newcomer to UC San Diego, but now he is also being honored as a (relative) newcomer to the United States. The Vilcek Foundation has named Knight the winner of a Creative Promise Prize in Biomedical Science for his "groundbreaking research on microbial communities and the development of computational tools that honed the analysis of microbial data." The Vilcek Foundation honors and supports foreign-born scientists and artists who have made outstanding contributions to society in the United States. Rob Knight was born in New Zealand, where he earned his bachelor's degree from the University of Otago in 1996, before going on to do his Ph.D. at Princeton University. While at the University of Colorado, Knight also became a Howard Hughes Medical Institute Early Career Scientist (2009-2014).

    In addition to his affiliation with the CSE department at UC San Diego, Knight (pictured center left with fellow recipients of Vilcek Prizes) is also a professor of pediatrics in the School of Medicine.  His computational and experimental approaches have led to rapid and cost-effective microbial DNA sequencing methods and data analysis platforms that help to understand similarities among microbial communities based on their evolutionary relationships.  Knight has used informatics to show how maps of distinct microbes thriving in different parts of the human body change over time, how human-associated microbes can influence metabolic health, and how microbes can be used as timekeepers to help establish the time of death in forensic examinations.  Knight is also continuing his work in bioinformatics, after a decade of developing software to analyze the abundance of microbial data that is now becoming available to researchers. Knight's recent book, "Follow Your Gut,"  was published by TED Books in April 2015.  Rob Knight was born in Dunedin, New Zealand. "New Zealanders tend to pride themselves on ingenuity and making do with whatever resources happen to be available," said Knight, but he is going beyond what's available to creating projects that encourage the public to contribute their individual microbiome data for future research and the greater good. He has set out to catalog the diverse kinds of microbes found in ecosystems across the globe in an ambitious, collaborative effort called the Earth Microbiome Project, but Knight is also a co-founder of the American Gut Project. For the latter project, anyone in the U.S. can contribute $99 and a personal sample to have their gut microbiome analyzed (and contributed to the growing store of data available to researchers).

  • CSE Alumni Brief Students on Profits, Perils in Tech Startups

    Lindsey Fowler (BS ’05), president of the CSE Alumni Advisory Board, moderated an April 2 panel of six alumni experts and Jay Kunin, executive director of the Moxie Center for Student Entrepreneurship at UC San Diego. The alumni included Taner Halicioglu (BS ’96), Jennifer Arguello (BS ’00), Chris Schulte (MS ’05), Aaron Liao (BS ’05), Erik Buchanan (BS ‘07), and Justin Allen (BS ’10), several of whom also sit on the alumni board.

    Justin Allen worked for Teradata after graduation, then joined a Bay Area startup called WebAction in 2014. He now works remotely from San Diego on purpose-built analytics applications in the growing real-time data streaming space. “I’m still a field engineer but I’m working on analytics applications and I get to live in San Diego while working for a startup,” said Allen. “It’s the best of both worlds.”

    Jennifer Arguello worked at four startups over the course of eight years. The last one (Tellme Networks) was acquired by Microsoft, where she worked for nearly five years before becoming a product manager at Mozilla. She says that she found a unique opportunity in a hybrid venture, combining some for-profit venture capital with non-profit activities to create positive social impact (along with economic value). Arguello calls her current employer, the Kapor Center for Social Impact, a “non-profit, social-good startup,” where she is a Senior Tech Advisor. Asked whether doing a non-profit startup is different from a for-profit venture, Arguello first points to what they have in common. “In both cases you’re begging for money,” she says, only half-jokingly.  “In fact, social entrepreneurism can be even more flexible and easier to do if it’s for profit.” Arguello also sits on the advisory boards of organizations that promote programming education, including Yes We Code, and Globaloria.

    When it comes to startups, advised the Moxie Center’s Kunin, both non-profits and for-profit companies need money in the bank. “Either way,” he said, “you need some kind of revenue model.”

    Chris Schulte was working at SAIC when he began to think about starting a company. “I was able to work on a startup in my spare time, mainly in the evening, while I was also working full-time for SAIC,” said Schulte. He became CTO and cofounder of MyCase, Inc., which made management software for law practices. Schulte stayed on when the company was acquired in 2012 by AppFolio. Recently, he left the company to think about the future. “Now I’m on an unspecified vacation,” he told the CSE students.

    Alumni Board president Fowler, who works for online retail giant Amazon, warned students to be careful about working on a startup from the comfort of a full-time company job: “You have to make sure that your employer doesn’t have any claim on your idea,” said Fowler, “especially if the future business is in some way related to your current job.”

    After graduating with a major in computer engineering, Aaron Liao worked at Microsoft for six years. He is currently the “evangelism director” at BitTorrent, and once again, he’s “starting to look for new startup opportunities.” Liao and others were asked about the biggest difference between working for a startup and working at a large, established company. “In a startup you wear many hats,” said Liao. “At Microsoft my job was very defined.”

    “A startup company also means that you really own the company’s success or failure – you’re more invested in what happens,” added Erik Buchanan, engineering lead and “startup entrepreneur” at Connectifier, who worked at multiple large enterprises before the startup, including Microsoft, Intuit, and Google. “What happens at a big company still matters, but you don’t feel it so personally.”

  • Alvarado Receives Engagement Excellence Award

    CSE Prof. Christine Alvarado will be honored in late May at the Summit on Women and IT organized by the National Center for Women & Information Technology (NCWIT). The summit will take place in Hilton Head Island, South Carolina, where Alvarado and three former colleagues at Harvey Mudd College will share in NCWIT's Engagement Excellence Award. The annual award recognizes authors whose curricular materials have been submitted to the elite EngageCSEdu collection. Winners must demonstrate excellence in computer-science content and pedagogy while also using research-based engagement practices to make computer science relevant and meaningful for students.
    The award highlights the pioneering work that CSE's Alvarado (at right) did at Harvey Mudd prior to joining the UC San Diego faculty in 2012. Her co-winners of the award were fellow computer science faculty Geoff Kuenning, Ran Libeskind-Hadas and Zachary Dodds, all still at Harvey Mudd. "The work I did with my colleagues at HMC was both about rethinking curriculum as well as creating a supportive and relevant structure and community in which students can learn," says Alvarado, noting that the award-winning work is also reflected in various efforts that she has undertaken at UCSD. 
    Those efforts include the establishment of a curriculum for the new Summer Program for Incoming Students (SPIS). Alvarado and fellow teaching professor Mia Minnes based the SPIS computer science curriculum on Harvey Mudd's CS5.  Alvarado notes, "Using CS5 as the backbone for the SPIS CS curriculum was a great way to give students an overview of the big picture of computer science and math, and to show both the real-world relevance of the material and the connections across the ideas that are normally segregated into different classes."
    Another effort benefiting from Alvarado's previous experience at HMC is the Early Research Scholars Program, which places first- and second-year CSE students in research apprenticeships with active research projects in CSE. "We are trying to build community between early undergraduates and grad students and faculty," she adds. "This way, students can not only see the relevance of what they are learning in their early courses, but they also form a deeper sense of belonging within CSE."
  • NSF Graduate Research Fellowships to CSE Students

    Three current CSE students are among the 2,000 nationwide to be offered 2015 Graduate Research Fellowships from the National Science Foundation (NSF). Graduate students Rachel Marty and Alexandria Shearer and graduating senior Max Shen were selected from among roughly 16,500 applicants this year. In addition, CSE undergraduate Antonella Wilby was a runner-up in the national competition, receiving an Honorable Mention for work in the field of robotics and computer vision. Shearer and Wilby are both in CSE Prof. Ryan Kastner's research group, which is already home to three NSF graduate fellows: Dustin Richmond, Perry Naughton, and Alric Althoff. Max Shen works in the bioinformatics group of CSE Prof. Pavel Pevzner, while Rachel Marty is also pursuing a Ph.D. in bioinformatics.

    With its emphasis on support of individuals, the NSF program offers fellowship awards directly to graduate students selected through a national competition. If accepted, the award provides three years of financial support within a five-year fellowship period ($34,000 annual stipend and $12,000 cost-of-education allowance to the graduate institution) for graduate study that leads to a research-based master's or doctoral degree in science or engineering.

    Rachel Marty (left) is a CSE alumna (BS '14) who earned her computer science degree with a specialty in bioinformatics. She graduated magna cum laude even while playing varsity collegiate basketball. Marty has done bioinformatics internships at Thermo Fisher Scientific (and Life Technologies, which it acquired) as well as at Illumina, where she developed an "application to centralize the experience of gene exploration for researchers." Her research interests include cancer genomics, genomic algorithms and population genetics. Marty has done research with both CSE Prof. Vineet Bafna (in the field of genomic algorithms) and with Hannah Carter at the UC San Diego School of Medicine's Division of Medical Genetics (on cancer genomics). "I will likely choose one of them to be my advisor at the end of the year," she says, when the rotation period of her doctoral program ends. Marty also CSE Prof. Andrew Kahng, who recommended her for the fellowship; as an undergrad, she took an algorithms class with Kahng, who also supervised an independent study project when she interned at Life Technologies. "He has played a prominent role in getting me where I am," notes Marty, who plans to finish her Ph.D. in 2019.

    Alexandria Shearer (right) is a Ph.D. student working on applications in heterogeneous computing. Less than two weeks ago, she was selected to receive a one-year UC San Diego Frontiers of Innovation Scholarship to continue her work on aerial LiDAR scanning of Mayan ruins. The FISP fellowship will cover Shearer over the summer and partially cover some equipment and travel costs related to her research, while the NSF stipend covers her primary expenses during the school year and the tuition allowance is paid directly to UCSD. Shearer arrived at UC San Diego in 2013 after getting her B.S. in computer science and engineering from Santa Clara University's School of Engineering, where she graduated as the top senior in computer engineering. Shearer expects to complete her Ph.D. in 2018. Among past honors, she was a SWE ViaSat Scholar in 2012, and a Google Anita Borg Memorial Scholar in 2011, the same year she won an NSF Grace Hopper Celebration Scholarship.

    Max Shen (left) will graduate this June with a B.S. in computer science and a specialization in bioinformatics. He is a research assistant in the group of CSE Prof. Pavel Pevzner, and for the past year has been a content contributor to Pevzner's Rosalind platform for learning bioinformatics and programming through problem-solving. For Rosalind, Shen designs and implements bioinformatics programming assignments onto a live website with randomized input generation and scoring. Rosalind is used in undergraduate bioinformatics courses, and also by students enrolled in Pevzner's massive open online courses on Coursera, including courses on bioinformatics algorithms. In addition to being a research assistant, Shen has also been a TA and tutor in CSE, a software engineering intern at Qualcomm, and a software engineer at Illumina. He was also a research assistant in the UC San Diego School of Medicine's Radiology Imaging Laboratory, thanks to which Shen may be the only computer science student who is also certified to operate a magnetic resonance imaging (MRI) machine.    

    Honorable Mention recipient Antonella Wilby is a graduating senior. She has been active for over two years in the Engineers for Exploration program co-directed by CSE's Kastner. Wilby graduates in June and will start grad school in CSE this fall, having just accepted an invitation to join Shearer in Kastner's research group. She also recently received a National Geographic Young Explorer grant for her work to document the endangered vaquita, a rare species of porpoise found primarily in the Gulf of California.

  • Disaggregating Data Centers

    CSE Prof. George Porter is back from the big annual Optical Fiber Conference (OFC) and expo, which took place in Los Angeles this year. The associate director of UC San Diego’s Center for Networked Systems (CNS) and two colleagues from the ECE department – Shaya Fainman and George Papen – were on the organizing/steering committee of a day-long industry workshop March 22. The topic: “Photonics for Disaggregated Data Centers.” The workshop – funded by NSF's Center for Integrated Access Networks (CIAN) and the Optical Society's Industry Development Associates trade group – explored the intersection of two relatively new research areas: data center networking, and disaggregated server design. 

    Large-scale Internet data centers host tens or hundreds of thousands of servers, powering sites such as search engines, social networks, streaming video services, shopping and healthcare.  The cost and energy demands of such facilities depend heavily on how efficiently the servers can work together, which in turn depends on the quality of the network interconnecting them.  “As servers get faster and faster, the demands placed on the data center network get increasingly hard to meet,” says Porter. “Industry is increasingly moving to fiber optics and photonics as a technology that can meet these incredible bandwidth requirements.  A major topic of our workshop involved understanding how to develop next-generation photonics to power the requirements of data center networks.”

    The workshop (left) also grappled with understanding the networking requirements for building disaggregated data centers – which, according to Porter, “re-evaluates” the entire concept of what a server is.  “Today a server represents a fixed combination of compute, memory, storage, and IO,” he explains. “As we look at the requirements for next-generation data centers, we see that the applications run in them have very dynamic requirements.” Porter cites the case of  Facebook, which may need servers with tons of memory that can be used to analyze billion-node graphs.  Alternatively, they may need servers with significant amounts of network IO that can power a caching layer. “Rather than build these as separate systems, with a disaggregated design, the individual components making up a server can be put directly on the network itself,” notes Porter. “Then a ‘server’ is simply a temporary binding of these resources together to work together for a specific purpose.  When those requirements change, different combinations of resources can be formed.  This vision is very powerful, but puts incredible strain on the network.” 

  • Society Honors Computer Scientist and Mathematician Fan Chung Graham

    CSE Prof. Fan Chung Graham and 30 others worldwide have been named as the Class of 2015 Fellows of the Society for Industrial and Applied Mathematics (SIAM). She was cited for her contributions to “combinatorics, graph theory and their applications,” and those applications have included Internet computing, communication networks, software reliability and more.

    The Distinguished Professor has joint appointments in CSE and the Department of Mathematics, where she holds the Paul Erdös Chair in Combinatorics. In the early 1990s, Chung Graham served on the council of SIAM.

    She is not the only Graham to be honored by SIAM – not even in the Graham household. That’s because her husband and fellow CSE professor, Ronald Graham, was honored in 2009 to be included in the inaugural class of SIAM Fellows. Ron Graham is also Chief Scientist in the California Institute for Telecommunications and Information Technology (Calit2).

    In 2013, Chung Graham and her husband were recruited to the inaugural class of Fellows of the American Mathematical Society. Both are experts in theoretical computer science and combinatorics.  Among her other honors, Chung Graham received the Allendoerfer Award from the Mathematical Association of America in 1990, and she is one of three CSE professors awarded membership in the American Academy of Arts and Sciences. (The others? Larry Smarr and... Ron Graham).

    Chung Graham earned her Ph.D. in mathematics from the University of Pennsylvania in 1974. She went on to work at Bell Labs in its Mathematical Foundations of Computing department.

  • Cyber Privacy App Gets Boost from CSE Alumnus, Research Scientist Now Teaching at Carnegie Mellon

    CSE got a plug from one of its alumni and former research scientist in an article about how most apps don't care about privacy. CSE alumnus Yuvraj Agarwal (Ph.D. '09) left UC San Diego in 2013 to be an assistant professor of computer science at Carnegie Mellon University, where he founded that university's Systems Networking and Energy Efficiency Lab. But when interviewed by the Pittsburgh Post-Gazette for a piece on privacy and apps, Agarwal noted that his team at UCSD had developed an app called Protect My Privacy in 2012, at a time when Apple had not yet offered its AppOpps rival. "Protect My Privacy sends user notifications when an app attempts to access location data, contacts or other information with the phone,"  noted Agarwal (pictured at UCSD demonstrating the app). Protect My Privacy, however, goes beyond what AppOpps can do, by intercepting communication between the app and the phone before any information is lost.

    On the downside, Protect My Privacy can only work on iPhones that have been modified to allow customization, or that have been 'jailbroken.'  Even so, Agarwal confirmed that an iOS 8 version of Protect My Privacy was released in late March, and since its launch, the app has been downloaded more than 200,000 times. However, as people load more and more apps on their smartphones, they can generated potentially hundreds of alerts per day that may require the user to say yes or no to a request for information. Agarwal is quoted admitting that, "it can get overwhelming pretty quickly."

  • New Opportunities for CSE Students, Faculty in Qualcomm Institute Innovation Space

    The Qualcomm Institute is setting up a new space where companies can apply to lease offices or labs on the second floor of Atkinson Hall, across from the CSE building. The institute announced the first seven companies that have been approved to be the first tenants of the facility, with more in the queue. The space is not an incubator, but it's a natural home for faculty, staff or student startups, because it allows a founder to locate startup staff within easy walking distance from the faculty member's departmental office. The Qualcomm Institute Innovation Space (QIIS) was also designed to work closely with other campus units that make up the entrepreneurial ecosystem of UC San Diego, including venture capital funds (Triton Fund, UC Ventures), the Moxie Center for Student Entrepreneurship, The von Liebig Entrepreneurism Center, The Basement (the recently-launched incubator/accelerator program for student entrepreneurs), etc. 

    In addition to three faculty startups (Sinopia Biosciences, STEAM Engine and VirBELA) and three early-stage companies that collaborate closely with researchers on campus (Comhear, Technosylva and RAM Photonics), QIIS is now home to the Foundation for Learning Equality (FLE), launched by a team of undergraduate and graduate students including recent cognitive science alumnus Jamie Alexandre (pictured center back row). “It’s estimated that one in three children worldwide lacks access to a quality basic education,” said Alexandre. “Sixty percent of the global population lacks the connectivity needed to access online education, so we have been developing an offline version of Khan Academy. Since being launched in December of 2012, the open-source platform, KA Lite, has now been installed in more than 140 countries and is used by thousands of schools, orphanages, community centers, refugee camps and prisons.” The offline server can be downloaded and run on a basic device such as a Raspberry Pi or even on aging Windows PCs, then other devices nearby can connect to that server to access the Khan Academy videos. A teacher with a single server can provide a classroom of 35 students with simultaneous access to KA Lite, and track their progress using teacher dashboard tools to enable them to most effectively intervene and help students who are struggling. By being located in Atkinson Hall, FLE gets proximity to the population of student programmers it needs in order to keep rolling out enhancements of KA Lite, and CSE students are already actively engaged. Current interns and student workers from CSE include undergraduates Teresa Do, Christine Pham (all class of '15), as well as Chris Li and Antriksh Yadav (both class of '16). Also working on KA Lite, CSE grad student Srishty Agrawal (MS '16), and cognitive science major David Canas, who is minoring in computer science.

    Read the Qualcomm Institute Innovation Space news release.
    Learn more about FLE and its current team members.

  • Bioinformatics Experiment Holds Promise for Industrial Production of Algae Biofuels

    CSE Prof. Vineet Bafna was on the roster of experts who spoke at the Green Revolution 2.0 symposium March 12-13 in the Qualcomm Institute, organized by the California Center for Algal Biology and the Center for Food and Fuel for the 21st Century. The bioinformatics expert addressed the “Ecology of Open Algae Ponds for the Production of Biofuels,” noting that algae are great feedstocks for biofuels and other products, but the challenge is to get yield at low cost. (In principle, microalgae may produce between 10 and 100 times more oil per acre than traditional crops, but that has not been achieved in an industrial setting.) “There is a general understanding in ecology that diversity is good for productivity, and that precept might be useful for industrial production,” explains Bafna. “But we don’t know that these ecological ideas can work in an industrial setting.”

    To test his hypothesis, Bafna’s team did a year-long experiment in which they monitored the prokaryotic and eukaryotic composition of an algae pond (pictured), using genome sequencing to assess the taxonomic composition and diversity in the pond. In addition to genomic sampling, they used phenotyping to gauge various measures of pond health. “We managed to optimize productivity of biomass over the course of a year,” says Bafna. “Our results strongly suggest that diversity is important for pond productivity, and even in a managed setting, open ponds behave like natural ecosystems.” The team’s results, as Bafna explained to the FF21 annual conference, indicate that algal diversity promotes production, and that understanding the ecology of open algae ponds for the production of biofuels is critical to managing their output of biomass energy and other products. The study was funded by NSF and carried out in a partnership with FF21 director Stephen Mayfield and Biological Sciences professor Jonathan Shurin (both from UC San Diego). Bafna also thanked collaborators at Sapphire Energy, Life Technologies and SDSU.

    Read the news release about the Green Revolution 2.0 symposium.

  • March 30 Application Deadline for Gordon Engineering Leadership Scholars

    CSE undergraduate and graduate students are eligible to apply for the Gordon Scholars Program. Organized by the Gordon Engineering Leadership Center, the program expects to select 20 students for the 2015-2016 program, half undergrads, half grad students. Applications for the prestigious scholarships are now available, and the selection committee expects the review and selection process to be very competitive.

    All applicants to the Gordon Center will be asked to prepare an application package consisting of:

    • A cover letter focusing on your perspective on engineering leadership;
    • Grad students must submit a CV with a list of publications or resume;
    • Undergraduates must submit a resume;
    • Video or in-person interview (to be scheduled after application is complete); and
    • Two letters of recommendation should highlight the student's academic progress and engineering leadership potential;

                  - For Ph.D. applicants, one recommendation letter must be from your advisor; or
                  - For Master's applicants, at least one recommendation letter must be from a faculty member.

    The final deadline to submit the online application is Monday, March 30, 2015.

    Students can apply at:

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