Googling the Googlers\' DNA: A Demonstration of the 23andMe Personal Genome S...

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Google Tech Talks May, 7 2008 ABSTRACT Introduced last November, the 23andMe Personal Genome Service offers customers a glimpse at their own DNA sequence, a 750-megabyte string of four characters (A, C, T and G) that functions as the operating system for a human being. Common variations in this code can influence the structure and function of the associated wetware in predictable ways. Some of these variations and their effects on traits such as athletic talent, pain sensitivity and avoidance of errors will be discussed in reference to three well-documented examples (Sergey Brin, Larry Page and Eric Schmidt). Have questions? 23andMe will have their Ancestry and Gene Journal specialists handy to answer all levels of questions. Want Your Own Genome? You can order it at the Spit Party for a significant discount (50% off)! Can't wait to spit? They will have kits available at the event for you to purchase and spit right there. If you happen to miss this party, the discount will be available for 24 hours after the event as well. You are encouraged to visit www.23andme.com, sign up for a demo account and take 23andMe for a test drive! This talk will be taped. Speaker: Linda Avey Linda has over 20 years of sales and business development experience in the biopharmaceutical industry in San Francisco, Boston, San Diego, and Washington, D.C. Prior to starting 23andMe, she developed translational research collaborations with academic and pharmaceutical partners for Affymetrix and Perlegen Sciences. Linda also spent time at Spotfire helping scientists understand the power of data visualization and at Applied Biosystems during the early days of the human genome project. The advent of high density genome-wide scanning technologies brought huge potential for significant discoveries. However, the lack of sufficient funding to enable adequate studies prompted Linda to think of a new research model. These ideas led to the formation of 23andMe. Her primary interest is the acceleration of personalized medicine, using genetic profiles to target the right drug to the right person at the correct dose. Linda graduated from Augustana College with a B.A. in biology.

Seattle Conference on Scalability: CARMEN: A Scalable Scienc

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Google Tech Talks June 14, 2008 ABSTRACT CARMEN is a $9M project building a scalable science cloud. Its focus is on supporting neuroscientists who will use it to store, share and analyze 100s of TBs of data. Understanding how the brain works is a major scientific challenge which will benefit medicine, biology and computer science. Globally, over 100,000 neuroscientists are working on this problem. However, the data that forms the basis for their work is rarely shared even though it is difficult and expensive to produce. The CARMEN project (www.carmen.org.uk) is addressing these challenges by developing a scalable cloud architecture to enable data sharing, integration, and analysis supported by metadata. An expandable range of services are provided in the cloud to extract value from raw and transformed data. This promotes the sharing of analysis services as well as data, and allows services to execute close to the data on which they operate. This is essential to avoid having to ship vast quantities (TBs) of data out of the cloud to the user's machine for analysis. Internally, the CARMEN cloud is built as a set of Web Services. Through experience of a wide variety of e-scientific projects over the past 8 years, we have identified a core set of generic services that we believe are needed to support science. These services, their scalability issues and novel features are: - Data repository. Most of the primary data is time series signal data. Searching for patterns (such as neuronal spikes) is a key requirement. CARMEN uses a novel parallel search infrastructure to find patterns quickly, even in vast quantities of data. - Metadata repository. Users need to be able to quickly search metadatametdata describing tens of thousands of datasets in order to locate data that is of interest. Ontologies are used to structure experimental metadata, and techniques are needed to quickly search this type of data. - Service repository and dynamic deployment. A novel feature of the architecture is that the analysis services are stored in a repository in the cloud. Users can write services in a variety of languages, package them as web services and then upload them into the cloud. These are then dynamically deployed on compute nodes as required to meet user requests. - Workflow Enactment Engine. Users can build workflows from the available services in order to orchestrate the entire process of analysis. These are then executed in the cloud. - Security. Scientists wish to control precisely who has access to their data and services. This service ensures that these desires are met. The talk will describe the design of the CARMEN system and show how it addresses the key scalability issues. It will cover the cloud services, explaining how each is designed to scale up to support thousands of users analysing TBs of data. We will present results from the CARMEN prototype to illustrate solutions and issues. Speaker: Paul Watson Paul Watson is Professor of Computer Science and Director of the North East Regional e-Science Centre. He graduated in 1983 with a BSc (I) in Computer Engineering from Manchester University, followed by a PhD in 1986. In the 80s, as a Lecturer at Manchester University, he was a designer of the Alvey Flagship and Esprit EDS systems. From 1990-5 he worked for ICL as a system designer of the Goldrush MegaServer parallel database server, which was released as a product in 1994. In August 1995 he moved to Newcastle University, where he has been an investigator on research projects worth over $20M. His research interests are in scalable information management, in particular parallel database systems and data-intensive e-science. Slides for this talk are available at http://groups.google.com/group/seattle-scalability-conference

Quicksilver: Universal Access and Action

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Google Tech Talks August 30, 2007 ABSTRACT Quicksilver hides almost unbounded power beneath the interface of a keyboard-driven launcher. Using a basic grammatical model, it allows you to move beyond basic search and work effortlessly with applications, data, and the web. Quickilver is above all a prototype intended to explore new forms of interaction. In this talk, we will explore the motivation behind Quicksilver, highlights of its implementation, lessons learned from its design, and the ways it might inform the future of navigation for the desktop and the web. Speaker: Nicholas Jitkoff Credits: Speaker:Nicholas Jitkoff

Think faster focus better and remember moreRewiring our brain to stay younger...

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Google Tech Talks June 16, 2008 ABSTRACT Explore the brain's amazing ability to change throughout a person's life. This phenomenon—called neuroplasticty—is the science behind brain fitness, and it has been called one of the most extraordinary scientific discoveries of the 20th century. PBS had recently aired this special, The Brain Fitness Program, which explains the brain's complexities in a way that both scientists and people with no scientific background can appreciate. This is opportunity to learn more about how our minds work—and to find out more about the latest in cutting-edge brain research, from the founder of Posit Science and creator of the Brain Fitness Program software, Dr. Michael Merzenich. Speaker: Dr. Michael Merzenich, Ph.D. Michael M. Merzenich, PhD: Chief Scientific Officer Dr. Merzenich leads the company's scientific team. For more than three decades, Dr. Merzenich has been a leading pioneer in brain plasticity research. He is the Francis A. Sooy Professor at the Keck Center for Integrative Neurosciences at UCSF. Dr. Merzenich is a member of the National Academy of Sciences. He is the recipient of numerous awards and prizes, including the Ipsen Prize, Zulch Prize of the Max Planck Institute, Thomas Alva Edison Patent Award and Purkinje Medal. Dr. Merzenich has published more than 200 articles, including many in leading peer-reviewed journals, such as Science and Nature. His work is also often covered in the popular press, including the New York Times, the Wall Street Journal, Time and Newsweek. He has appeared on Sixty Minutes II, CBS Evening News and Good Morning America. In the late 1980s, Dr. Merzenich was on the team that invented the cochlear implant, now distributed by market leader Advanced Bionics. In 1996, Dr. Merzenich was the founding CEO of Scientific Learning Corporation (Nasdaq: SCIL), which markets and distributes software that applies principles of brain plasticity to assist children with language learning and reading. He is an inventor on more than 50 patents. Dr. Merzenich earned his BS degree at the University of Portland and his PhD at Johns Hopkins.

A quantum computer can determine who wins a game faster than a classical comp...

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Google Tech Talks April, 2 2008 ABSTRACT Imagine a game where two players go back and forth making moves and at the end of a fixed number of moves the position is either a win or a loss for the first player. In this case, if both players play best possible, it is determined at the first move who wins or loses. To figure out who will be the winner you need not look at all of the N final positions but only at N^0.753. I will show that with a quantum computer the exponent can be reduced to 0.5. The technique involves quantum scattering theory and illustrates how ideas from physics can be used to design quantum algorithms that outperform even best possible classical algorithms. Speaker: Edward Farhi Professor of Physics; Director, Center for Theoretical Physics Massachusetts Institute of Technology Research Interests: Edward Farhi was trained as a theoretical particle physicist but has also worked on astrophysics, general relativity, and the foundations of quantum mechanics. His present interest is the theory of quantum computation. As a graduate student, Farhi invented the jet variable "Thrust," which is used to describe how particles in high energy accelerator collisions come out in collimated streams. He then worked with Leonard Susskind on grand unified theories with electro-weak dynamical symmetry breaking. He and Larry Abbott proposed an (almost viable) model in which quarks, leptons, and massive gauge bosons are composite. With Robert Jaffe, he worked out many of the properties of a possibly stable super dense form of matter called "Strange Matter" and with Charles Alcock and Angela Olinto he studied the properties of "Strange Stars." His interest then shifted to general relativity and he and Alan Guth studied the classical and quantum prospects of making a new inflationary universe in the laboratory today. He, Guth and others also studied obstacles to constructing a time machine. More recently, Farhi has been studying how to use quantum mechanics to gain algorithmic speedup in solving problems that are difficult for conventional computers. He and Sam Gutmann proposed the idea of designing algorithms based on quantum walks, which has been used to demonstrate the power of quantum computation over classical. They, along with Jeffrey Goldstone and Michael Sipser, introduced the idea of quantum computation by adiabatic evolution, which has generated much interest in the quantum computing community. This group was tied for first in showing that there is a problem that cannot be sped up by a quantum computer. In 2007, Farhi, Goldstone and Gutmann showed that a quantum computer can determine who wins a game faster than a classical computer. Edward Farhi continues to work on quantum computing but keeps a close eye on particle physics and recent developments in cosmology. Biographical Sketch: Edward (Eddie) Farhi went to the Bronx High School of Science and Brandeis University before getting his Ph.D. from Harvard in 1978. He was then on the staff at the Stanford Linear Accelerator Center and at CERN in Geneva Switzerland before coming to MIT, where he joined the faculty in 1982. Farhi has given lectures on his own research at many of the major physics research centers in the world. At MIT, he has taught undergraduate courses in quantum mechanics and special relativity. At the graduate level he has taught quantum mechanics, quantum field theory, particle physics and general relativity. Farhi won three teaching awards at MIT and in 2000, 2001, and 2002 he lectured the big freshman physics course, "8.01." In July 2005, he was appointed the Director of MIT's Center for Theoretical Physics. Selected Publications: Professor Farhi's publications are available online from the SPIRES HEP Literature Database (particle physics) and arXiv.org e-Print archive (quantum computing).

An Overview of High Performance Computing and Challenges for the Future

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Google Tech Talks January, 25 2008 ABSTRACT In this talk we examine how high performance computing has changed over the last 10-year and look toward the future in terms of trends. These changes have had and will continue to have a major impact on our software. A new generation of software libraries and algorithms are needed for the effective and reliable use of (wide area) dynamic, distributed and parallel environments. Some of the software and algorithm challenges have already been encountered, such as management of communication and memory hierarchies through a combination of compile--time and run--time techniques, but the increased scale of computation, depth of memory hierarchies, range of latencies, and increased run--time environment variability will make these problems much harder. We will focus on the redesign of software to fit multicore architectures. Speaker: Jack Dongarra University of Tennessee Oak Ridge National Laboratory University of Manchester Jack Dongarra received a Bachelor of Science in Mathematics from Chicago State University in 1972 and a Master of Science in Computer Science from the Illinois Institute of Technology in 1973. He received his Ph.D. in Applied Mathematics from the University of New Mexico in 1980. He worked at the Argonne National Laboratory until 1989, becoming a senior scientist. He now holds an appointment as University Distinguished Professor of Computer Science in the Electrical Engineering and Computer Science Department at the University of Tennessee, has the position of a Distinguished Research Staff member in the Computer Science and Mathematics Division at Oak Ridge National Laboratory (ORNL), Turing Fellow in the Computer Science and Mathematics Schools at the University of Manchester, and an Adjunct Professor in the Computer Science Department at Rice University. He specializes in numerical algorithms in linear algebra, parallel computing, the use of advanced-computer architectures, programming methodology, and tools for parallel computers. His research includes the development, testing and documentation of high quality mathematical software. He has contributed to the design and implementation of the following open source software packages and systems: EISPACK, LINPACK, the BLAS, LAPACK, ScaLAPACK, Netlib, PVM, MPI, NetSolve, Top500, ATLAS, and PAPI. He has published approximately 200 articles, papers, reports and technical memoranda and he is coauthor of several books. He was awarded the IEEE Sid Fernbach Award in 2004 for his contributions in the application of high performance computers using innovative approaches. He is a Fellow of the AAAS, ACM, and the IEEE and a member of the National Academy of Engineering.

Radioactive astronauts: images worth a thousand experiments.

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Google Tech Talks April, 22 2008 ABSTRACT Cosmic radiation presents a very real threat to astronauts. As part of a NASA funded project to evaluate the cancer risks of a trip to Mars, Dr. Costes' team has been collecting hundreds of gigabytes of 3D and 4D imagery showing the traversal of cosmic particles in human cells, and characterizing the DNA damage along those tracks to reveal the existence of DNA repair factories. In addition to sharing his project with us, Dr. Costes will discuss how they've overcome some of the challenges in 3D image registration and segmentation, pattern recognition and classification, and storing, organizing and browsing through thousands of images and experimental measurements. Speaker: Sylvain Costes Dr. Costes is a principal investigator in the Life Sciences Division of the Lawrence Berkeley National Laboratory.

The Bloom filter

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Google Tech Talks November, 15 2007 ABSTRACT The Bloom filter, conceived by Burton H. Bloom in 1970, is a space-efficient probabilistic data structure that is used to test whether an element is a member of a set. False positives are possible, but false negatives are not. Elements can be added to the set, but not removed (though this can be addressed with a counting filter). The more elements that are added to the set, the larger the probability of false positives. For example, one might use a Bloom filter to do spell-checking in a space-efficient way. A Bloom filter to which a dictionary of correct words has been added will accept all words in the dictionary and reject almost all words which are not, which is good enough in some cases. Depending on the false positive rate, the resulting data structure can require as little as a byte per dictionary word. In the last few years Bloom filter become hot topic again and there were several modifications and improvements. In this talk I will present my last few improvements in this topic. Speaker: Ely Porat Ely Porat received his Doctorate from Bar-Ilan University in 2000. Following that, he fulfilled his military service and, in parallel, worked as a faculty member at Bar-Ilan University. Having spent the spring 2007 semester as a Visiting Scientist in Google, he is now back at Bar-Ilan University. The main body of Ely Porat's work concerns matching problems: string matching, pattern matching, subset matching. He also worked on the nearest pair problem in high-dimensional spaces as well as sketching and edit distance.

Mapping Travel Medicine

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Google Tech Talks February, 8 2008 ABSTRACT Emporiatrics or Travel Medicine is a discipline within medicine that prepares a traveler using vaccines, medicines and knowledge to avoid disease when visiting a foreign destination. I will discuss the current mapping of interventions offered to patients planning trips and illustrate with examples how the constraints of patient needs and the risks at a specific destination overlap to arrive at a list of recommendations that are offered a traveler before departure. Depending on crowd size I can run through personal case examples for those who are planning an exotic trip. I hope to also highlight limitations of the practice of emporiatrics and suggest where Google can potentially offer a useful "expert system" that might be modulated by risk, price points and insurance coverage using disease maps from publicly available surveillance data and patient records, using the Kaiser Epic Data system. Speaker: D. Scott Smith. Scott grew up in Boulder Colorado and attended medical school at the University of Colorado. He went to public health school at Harvard University where an interest in Tropical Public Health was further developed, leading to a year long adventure on a Fulbright scholarship in Cali, Colombia, seeking improved diagnostic technologies to understand the epidemiology of leishmaniasis, and onchocerciasis (River Blindness). He completed residency then a Fellowship at Stanford University in Medicine then Infectious Disease & Geographic Medicine. Scott practices at Kaiser in Redwood City, California where he heads the HIV/AIDS clinic and oversees the travel medicine services locally but also is developing regionalization of the Travel Medicine Services for Kaiser Northern California. He co-chairs the biennial National Conference on Preparing International Travelers. He teaches at Stanford Medical School in the Microbiology and Immunology Division and directs a course for undergraduates in Human Biology entitled "Parasites & Pestilence: Public Health Challenges". He was recently presented the Bloomfield award in recognition of excellence in the teaching of clinical medicine at Stanford School of Medicine. Acknowledging Candid's epiphany (after tumultuous world travel) that staying in one's own backyard is a pathway to happiness, in his spare time he gardens and keeps chickens and bees. As one's own content is not a final destination, he recently traveled with family to Uganda and South Africa to speak and visit an AIDS study site and to see family later this year. http://www.permanente.net/homepage/doctor/scottsmith/ http://www.stanford.edu/class/humbio103/

Social Recommendations

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Google Tech Talks April, 10 2008 ABSTRACT Social Recommendations will change both the lens through which we see the world as well as the manner in which we experience it. Everything from the media that we consume to the events we attend will be influenced by hyper-relevant results delivered through hierarchical social relationships. This talk demonstrates current efforts to integrate social relationships into recommended user experience including SoMR, the Social Media Recommendation API. Speaker: Dan Carroll Dan is the Director of the SoMR (Social Media Recommendation) project and the CEO of imp, the Intelligent Media Platform. Dan has worked in magazine and book publishing, labor organizing, and at a public policy think tank. He holds a patent in digital media distribution and writes the blog www.mediapatron.com. Dan lives in Mountain View, California and serves on the boards of Echolocations and InRadio.

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