“Rain or shine, Seattle has quickly become the center of the most intensive engineering in cloud computing: the design and management of global-scale data centers …
“Besides talent that knows how to build infrastructure, Seattle has a number of leading cloud software companies. Tableau Software, a leader in the computer visualization of large sets of data, is across the street from Google in Fremont. Concur, used for online expense forms, is in Bellevue, near Microsoft Azure. Other companies include Chef, which produces open source cloud automation software; Apptio, a cloud monitoring company, and Socrata, which stores and publishes over 100,000 data sets for 150 government organizations …
“Another factor is the growing presence of the University of Washington’s computer science department, now considered a leader in distributed computing. ‘There’s an argument that Seattle owns the cloud now,’ said Ed Lazowska, who holds the Bill & Melinda Gates chair in Computer Science & Engineering at the university. ‘Universities are always part of the axis’ in building out a regional tech center, he said.
“The university, which awards about 250 computer science degrees a year, is now working on courses in machine learning, which is how computers, particularly in the cloud, study and adapt based on big streams of data.
“‘The cloud and big data are closely connected,’Mr. Lazowska said. ‘We’re incredibly lucky to be in Seattle.'”
Wired writes: “A computer scientist at the University of Washington, Popović first became known for his popular online game, Foldit, which challenges players to create intricate protein patterns by bending and rearranging amino acids – the constituent units of proteins – into new shapes …
“Now Popović wants to put the power of games to an even better use. Earlier this year he adapted DragonBox, a Norwegian game app that introduces algebraic concepts with animal-faced cards, then builds up to numbers and computational signs … As harder concepts are introduced, students who need more time on a level get additional problems; those who understand it move on. In an experiment with DragonBox Adaptive in Washington state, an average of 93 percent of K–12 students successfully mastered concepts after only 90 minutes of gameplay, and they didn’t want to stop.
“Popović is using this method as the basis for an entire sixth-grade math curriculum in trial now in Seattle and next year in Brooklyn and Brazil. He’s banking on digital tablets to help teachers adjust their lessons to individual performance. Science, language arts, even coding are all on the table for the future. Finally, an argument for more screen time for kids.”
Read more in Wiredhere. Learn about UW CSE’s Center for Game Science here.
Ten years ago – on October 9th 2003 – we dedicated the Paul G. Allen Center for Computer Science & Engineering.
Designed by LMN Architects, the Allen Center – still widely regarded as the finest computer science facility in the nation – has had a dramatic impact on UW CSE’s competitiveness, allowing us to move forward into the 21st century as one of the nation’s leading computer science and computer engineering programs:
State-of-the-art laboratory space has changed the nature of our research. Annual research expenditures have tripled – from $7 million in the year prior to occupancy, to more than $20 million today. (Faculty increased by only 24% during this period – from 38 to 47.) The number of technical staff supporting research has more than doubled – from 23 to 58. We had only 2 postdoctoral research fellows in 2003 – we have 27 today. Interdisciplinary collaborations have flourished, reflecting the broad impact of the field in the modern university and the modern world.
Enrollments have increased, providing greater opportunity for Washington State students and driving the state’s technology industry. The pace has been slower than we would have liked – state support is required to increase enrollment, since tuition falls far short of covering costs. But in the past decade, undergraduate majors have increased from 430 to 650 (+50%); full-time graduate program majors from 142 to 222 (+55%); part-time professional masters program majors from 120 to 160 (+33%); and annual enrollment in our two introductory courses from 2,000 to 3,600 (+80%). Additional growth has recently been funded.
More than 200 friends and alumni donated a total in excess of $40 million to make the Allen Center a reality. We are grateful to Paul G. Allen, our lead donor; to Tom Alberg and Jeremy Jaech, the co-chairs of our development committee; to Bill & Melinda Gates and to Microsoft for gifts in excess of $5 million; and, indeed, to each and every donor, because each and every gift was essential. As we said at the time, we didn’t know 40 people who could provide $1 million each, and we didn’t know 40,000 people who could provide $1,000 each!
This extraordinary generosity continued after the completion of the Allen Center. In 2003, our departmental endowment (which supports faculty, graduate students, undergraduate students, and innovation across-the-board) totaled less than $6 million; today it is in excess of $40 million! Most recently, Jeff Bezos and Amazon.com provided two $1 million Amazon Professorships in Machine Learning to assist us in recruiting machine learning stars Emily Fox and Carlos Guestrin.
Today, the Allen Center is overflowing, and we are launching a new project to expand our space. Leadership in computer science is increasingly essential to the University of Washington’s broad-based competitiveness, to the vitality of our region, and to our nation’s ability to address its challenges and seize its opportunities. UW CSE remains committed to excellence and impact. “If it was just hot air, we’d still be in Sieg Hall.”
The School Leadership 2.0 blog reports on an interview with Bill Gates and Vicki Philips (Bill & Melinda Gates Foundation) during a recent visit to Atlanta.
“Now the foundation is working with the Center for Game Science at the University of Washington on a free, online game called Refraction. As students play, their progress is visible to the teacher on his or her computer, allowing the educator to see instantly what concepts students understand.
“The idea is that in coming years, there could be a digital mall full of low-cost or free online games teachers could download to use with the entire class or individual students.
“‘Part of what we’re trying to do is make more robust the array of things teachers have access to at their fingertips that are aligned to standards, that are high quality, that engage kids though technology and let [teachers] be the orchestra leader,’ Phillips said.
“It’s early in the development phase, and the foundation is still trying to figure out how to do this game-based technology well, Gates said.
“The foundation will play a role in researching and developing this new technology, work that isn’t likely to be done at the federal or state level.
“‘It’s definitely going to make a contribution,’ Gates said. ‘Motivation is such a huge part in what ends up differentiating student outcomes. Everyone has the ability to do fantastic work at a high school level. It’s just without the right teacher and the right motivation you don’t always get there.'”
Read more here. Learn about UW’s Center for Game Science here.
Reminder: Bill Gates will deliver the UW CSE Distinguished Lecture on Thursday at 3:30 in the Microsoft Atrium of the Paul G. Allen Center for Computer Science & Engineering. Details (including live webcast information) here.
Bill Gates III will deliver the UW Computer Science & Engineering Distinguished Lecture at 3:30 p.m. on October 27 in the Microsoft Atrium of the Paul G. Allen Center for Computer Science & Engineering:
The Opportunity Ahead: A Conversation with Bill Gates
Thursday, October 27, 2011
3:30pm, Microsoft Atrium, Paul G. Allen Center for Computer Science & Engineering
Reception to follow
Although space is limited, the event will be webcast live, and web archived. Additional information here.
Advances in both the quantitative and qualitative aspects of computing offer remarkable opportunities for contributions in every sphere. Coupled with advances in natural user interfaces and pervasive computing, the next decade could see significant breakthroughs that improve our world, particularly for the poorest two billion people on earth.
An effort by students and faculty from CSE, Human-Centered Design and Engineering, and the Information School to design a low-cost portable ultrasound system for use in the rural developing world has received a $100,000 “Grand Challenges Explorations” grant from the Bill & Melinda Gates Foundation – one of 65 grants awarded among more than 2,400 applicants.
Read the UW press release here. Read about the project and its participants here. Learn about Change, the cross-campus collaboration under which dozens of remarkable projects such as this take place, here. There’s a nice video describing the project here.
British scientist Rosalind Franklin, who spent the early 1950s researching the structure of DNA at King’s College London, should have won the Nobel Prize. She very well may have, except that her untimely death from ovarian cancer at the age of 37 meant that the Nobel Committee, which does not award posthumously, did not even consider her. For it was Franklin, not the famous scientific duo Watson and Crick, who captured the first image proving the shape of deoxyribonucleic acid — better known as DNA, the building block of all life.
At the time, Franklin was applying her expertise in x-ray crystallography to determine the structure of DNA in collaboration with King’s College Ph.D. student Raymond Gosling. The researchers captured an image of moistened DNA fibers using x-ray diffraction techniques and equipment refined by Franklin herself. The so-called Photo 51, which revealed a helical shape consisting of two strands, and other unpublished data from Franklin’s lab would find their way into the hands of fellow scientists James Watson and Francis Crick at Franklin’s alma mater, the University of Cambridge. The material confirmed the three-dimensional structure of DNA as a double helix — a structure the pair would race to describe in a paper published in April 1953 in the journal Nature.
Although Franklin would publish her own paper co-authored with Gosling on the double helix in the same issue, it was Watson and Crick, along with Franklin’s King’s College colleague Maurice Wilkins, who went on to share the 1962 Nobel Prize in Physiology or Medicine and thus ensure their places in the pantheon of scientific achievement. The contributions of Franklin, who had passed away 4 years before the Nobel announcement, would only begin to be more widely appreciated decades later. In any event, the Nobel Prize can only be shared by up to 3 individuals, so we will never know whether Franklin, had she lived long enough, would have received her due. Given the limitation on sharing the prize and the attitudes toward women in science at that time — and her own colleagues’ attitudes toward Franklin, in particular — it seems unlikely.
More than 60 years after Watson and Crick laid eyes on Photo 51, Allen School professor Luis Ceze met Seattle-based multimedia artist Kate Thompson in a bar not far from the University of Washington campus. Ceze co-directs the Molecular Information Systems Laboratory, a partnership between UW and Microsoft that is exploring synthetic DNA’s potential as a long-term storage solution and computational platform for digital data. He had already crossed paths with Thompson on campus, where she was doing an artist’s residency in the Nemhauser Lab focused on evolutionary biology. Ceze was intrigued by what she told him about her work, which is focused on making science visual.
For more than a year, he and his colleagues had been collecting images submitted by people around the world as part of the #MemoriesInDNA project under the tagline “What do you want to remember forever?” After meeting Thompson, Ceze became interested in exploring a way to ensure that the world would remember Franklin and her contributions forever — and he had a particularly fitting medium in mind.
“Rosalind Franklin was largely responsible for uncovering the structure of DNA, nature’s own perfected storage medium. Her work opened up a whole new avenue of scientific research and discovery for which, to this day, she does not really get the credit that she deserves,” Ceze said. “We had this massive collection of image files signifying what people want to preserve for posterity, and this new storage method. So we thought, why not use them to demonstrate the science we’ve been working on while paying tribute to the scientist who started it all?”
The idea he and Thompson hashed out over glasses of wine was elegantly simple. The lab would work with Thompson to create a piece of art to commemorate Franklin that incorporates the very medium that she revealed to Watson, Crick, and the world: DNA. To be precise, the medium would be synthetic DNA containing thousands of copies of images people had voluntarily contributed to advance a new wave of molecular systems research.
“I was fascinated by the idea of honoring this brilliant but mostly forgotten woman using the same material that should have made her famous in her own lifetime,” said Thompson, who took on the role of artist-in-residence at MISL after meeting with Ceze. “Until recently, her legacy to science and the world went largely unnoticed. I hope this project helps to ensure it will not be ignored.”
The result of Thompson’s collaboration with the MISL is now on display in the Bill & Melinda Gates Center for Computer Science & Engineering on the UW Seattle campus. The work, which measures 40 inches high by 30 inches wide and was created using acrylic ink on archival paper, took nearly 8 months from conception to completion. It is one of three original copies Thompson produced at the behest of the lab.
Viewed at a distance, the work is clearly a portrait of Franklin. Thompson reproduced her likeness from an old black and white photograph, combining soft, dark brush strokes with a mosaic of nearly 2,000 meticulously arranged images — the majority of which measure just ⅞ inch square — from the #MemoriesInDNA collection. The artist arranged the latter with the help of a macro she wrote for the purpose, which sifted through the images and sorted them by tonal values.
The images that make up Franklin’s face are contained within a larger collection that serves as a colorful backdrop for the subject of the painting. Up close, the images themselves come into sharper relief; if they linger long enough, viewers can make out the contents of the individual photos in detail. Each image depicts a person, place or object someone wants remembered in perpetuity.
But Thompson didn’t just paint on the images; she painted with them, infusing Franklin’s likeness with the actual data files ensconced in their microscopic storage medium. Using roughly half of the trove of more than 10,000 photos submitted as part of #MemoriesInDNA, MISL researchers first converted the digital image files — around 325 megabytes of data — into the As, Ts, Cs and Gs of DNA and encoded them into synthetic DNA ordered from Twist Bioscience. Thompson then took the vial of DNA furnished by the lab, which consisted of a mere 1.5 milliliters of liquid, and mixed the contents with black acrylic ink along with a binding substance that would help it adhere to the paper. She combined yet more of the image-laden DNA with a clear acrylic hardener, which she used to coat the finished piece.
“I painted several practice portraits using plain ink first,” the artist recalled with a laugh. “I didn’t want to mess up when it came time to use the real thing. Ink is relatively inexpensive but specially encoded DNA from a lab, not so much!”
Before Thompson could pick up her brush, lab members David Ward, Bichlien Nguyen, Xiaomeng Liu, and Jeff Nivala conducted experiments to ensure that, in the latter’s words, “the science was as rigorous as the art.” First and foremost, they needed to establish that no chemical reaction would occur between the synthetic DNA and acrylic medium when Thompson mixed the two in her studio. The team also wanted to be confident that, once mixed and applied to paper, the DNA could be subsequently retrieved from the material. The outcome is both a work of art and an artifact of science.
“Not that I’m suggesting you do this — in fact, please don’t! — but if you were to scrape a little bit of the portrait off, with the right equipment you could retrieve the data and convert it back from DNA molecules to digital 0s and 1s,” explained MISL co-director Karin Strauss, principal research manager at Microsoft Research and affiliate professor at the Allen School. “This portrait is not only preserving Franklin’s memory but preserving the data as well, in a form that will be accessible to future generations.”
To increase the likelihood that the data contained in the work will, indeed, be accessible for generations to come, the team built in a high degree of redundancy. Nguyen estimates it took 30 minutes to amplify copies of each image file using polymerase chain reaction, or PCR.
“Because DNA as a storage medium is so dense, we were able to provide Kate with around a trillion copies of each image to mix into the paint,” explained Nguyen, a senior researcher at Microsoft Research who oversaw the DNA storage process. “That way, we can be certain that we will be able to retrieve all of the data — even if a portion of one set of images is somehow lost or damaged, we still have many back-ups.”
This is not the first time that the MISL team has applied its science to the arts. The lab previously partnered with Twist Bioscience to preserve significant cultural and historical artifacts in DNA as a way of demonstrating its potential for archival data storage and retrieval, including iconic musical performances at the Montreux Jazz Festival, the top 100 books of Project Gutenberg, the Universal Declaration of Human Rights in 100 languages, and the non-profit Crop Trust’s entire seed database. Along the way, the team set a new record for the amount of digital data stored in and successfully retrieved in DNA that appeared in a peer-reviewed journal, presented new techniques for random access, developed a new platform for microfluidics automation for DNA data storage at scale, and demonstrated the world’s first end-to-end automated system for encoding digital data in DNA.
Members of the public may view the portrait of Franklin on the ground floor of the Bill & Melinda Gates Center, at the base of the Anita Borg Grand Stairway. The lab is also exploring the potential to exhibit the artwork in additional locations in the future to reach an even wider audience.
“Our team was excited to partner with Kate on this project, which highlights an often forgotten figure who helped usher in the age of molecular storage,” Ceze said. “I hope the artwork itself, the science upon which it’s based, and the story of Rosalind Franklin will inspire people.”
Read more about Thompson’s work here, and learn more about the MISL’s work on DNA data storage here. Read the original #MemoriesInDNA announcement here. The lab members and the artist would like to express their appreciation to the thousands of people, spread out over 80 countries, who shared their personal photos as part of the #MemoriesInDNA project. The lab will continue to use the images as part of its research to advance DNA-based computation and image search.
In this month’s Undergrad Spotlight, we check in with a student who may need no introduction to gaming fans. Kevin Ryoo — a second year Allen School student who transferred from Highline College — built a career as a world champion gamer before deciding to study computer science. In fact, according to Ryoo, playing games all day every day inspired his academic pursuits to learn how to design and build software. As his education advanced, his interest in computer vision, machine learning and artificial intelligence has grown. Ryoo has an upcoming internship with Shopify, after Tweeting about needing an internship. Shopify’s CEO Tobias Lütke saw it, and knowing about Ryoo’s professional gaming career, offered him an internship on the spot.
Allen School: When did you start gaming, and how did you become so successful at it?
Kevin Ryoo: I started playing games professionally when I was 14 years old. I played a game called Warcraft 3. Even back then (in 2002), it had a match-making system where you get matched with a player at the same skill level. I kept winning and my ranking improved. Eventually I was ranked in the top 16 and my name was on the first page of players. Because of that, pro-gaming teams reached out to me with offers. That’s how I first got into it.
I think I was able to become successful in gaming because I had the motivation and dedication to do my best. I really liked the feeling of winning a game — I hated losing, it was stressful to me. So I practiced a lot and whenever I lost, I watched the replay of the game to learn from my mistakes. I repeated it again and again and as a result, I was able to become a champion in multiple competitions. I worked hard to become a gaming nerd.
Allen School: How did you build a career in professional gaming, and how did it change your life?
KR: When I was 16 years old, I won a tournament called the World Cyber Games (WCG). It took place once a year and follows a structure similar to the Olympics, in which regional champions compete to represent their countries. In turn, those winners compete for international glory. By winning the tournament two years in a row, in 2005 and 2006, I became a world-renowned Esports gamer and was even inducted into the WCG Hall of Fame. After that, I quit gaming to finish high school. While waiting for my green card to go to college [Ryoo moved to the USA from Korea at the age of 16], I started to play Starcraft 2. As my ranking went up, I decided to do pro-gaming again. In Starcraft 2, I won a Blizzcon US Championship, which is my second biggest achievement, and I also got 2nd and 3rd place in Major League Gaming.
I really loved my pro-gaming life and learned a lot from it. I traveled the world, made new friends from interesting places and learned to appreciate humanity’s rich diversity. In addition to meeting gamers and fans on the road, I became a more effective communicator by becoming an online streamer on Twitch.tv. At any given moment, I would have roughly 7,000 people watching live on my Twitch streaming channel. I really enjoyed these sessions because, in addition to showcasing my craft, I could communicate with people from other countries, share opinions, and develop an appreciation for the things that make different groups unique and wonderful. Through this, I naturally became much more personable, social optimistic, and open-minded person. Unfortunately, I have no time to spend on gaming right now. But I am fine with it because I am motivated to study computer science, not gaming, at this moment.
Allen School: What do you find most enjoyable about being an Allen School student?
KR: The Allen School has all the resources that students need. The professors are great, the TAs have a lot of office hours, there are tons of tech-talks from top companies, a great career fair that also includes the top companies, amazing advisers, a new Bill & Melinda Gates Center to study in, and the labs have impressive equipment. I always feel so fulfilled by these resources and I never feel alone.
Allen School: What activities and interests do you have outside of your studies?