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Data Intensive Visual Engine for molecular simulation data Thursday, October 24, 4:00 pm in CSE-305

I won’t post all talks here, but occassionally we will.  If you want to see the full schedule of talks, you can go here:

http://www.cs.washington.edu/events/colloquia/

Please join the eScience Institute Thursday, October 24, 4:00 pm in CSE-305.  Refreshments will be provided.

Valerie Daggett (UW):

Valerie Daggett obtained her BA from Reed College in Portland Oregon in 1983. A couple of years later she went to the University of California, San Francisco for her PhD (awarded in 1990) and was then a postdoctoral fellow at Stanford University. She joined the faculty at the University of Washington in 1993 and has been there ever since. She is a professor in the Department of Bioengineering, College of Engineering and School of Medicine. She also holds adjunct positions in the Biochemistry Department and the Biomedical Health and Informatics Program. She has published over 220 papers and maintains active research programs in protein dynamics and folding, simulation, protein misfolding diseases, and the general area of bioinformatics. She is on a Senior Editor of Protein Engineering, Design and Selection as well as a board member for numerous other scientific journals.

DIVE: Data Intensive Visual Engine for molecular simulation data

Data-driven research is a rapidly emerging commonality throughout scientific disciplines. Recently, with the proliferation of inexpensive commodity computing clusters, synthetic data sources such as modeling and simulation are capable of producing a continuous stream of terascale data. Confronted with this data deluge, domain scientists are in need of data-intensive analytic environments. Dynameomics is a terascale simulation-driven research effort designed to enhance our understanding of protein folding and dynamics through molecular dynamics simulation and modeling. The project routinely involves exploratory analysis of 100+ terabyte datasets using an array of heterogeneous structural biology-specific tools. In order to accelerate the pace of discovery for the Dynameomics project, we have developed DIVE, a framework that allows for rapid prototyping and dissemination of domain independent (e.g., clustering) and domain specific analyses in an implicitly iterative workflow environment.

The information in the data warehouse is classified into three categories: raw data, derived data, and state data. Raw data are generated from simulations and models, derived data are produced through tools operating on the raw data, and state data constitute the record of the exploratory workflow, which has the added benefit of capturing the provenance of derived data.

DIVE empowers researchers by simplifying and expediting the overhead associated with shared tool use and heterogeneous datasets. Furthermore, the workflow provides a simple, interactive, and iterative data-oriented investigation paradigm that tightens the hypothesis generation loop. The result is an expressive, flexible laboratory informatics framework that allows researchers to focus on analysis and discovery instead of tool development.

Upcoming Seminars:

* November 6, 4 PM (233 Sieg Hall)

Clark Gaylord  (Virginia Tech)

Data Science Meets Infrastructure: Strategic Highway Research Program (SHRP 2)

October 18, 2013

security team – talk

Hi,

This talk is open to all ugrads:

This week’s UWctf (Batman’s Kitchen) meeting is on Wednesday, 9 October, at 5:30p in CSE room 303.  Amanda Crowell from iSEC will give a talk about her job in a security company.  Her talk will cover:

        * Her path to the security industry (she didn’t know what C++ was when she first stepped foot into college)

        * What is “security”?   What does it mean?  What kinds of security are there?  What kinds of defenses are there?

        * What’s it like to be a consultant?

        * The Seattle security scene

See you Wednesday!

Melody Kadenko, Batman’s Kitchen Advisor

Computer Science & Engineering

October 7, 2013

Tomorrow: Google (X) Glass talk and Google APM talk

 

Both of these events are TOMORROW,  Wednesday 10/2/2013

Please RSVP: http://goo.gl/s98FR8

 

Google Glass Talk – EE125, 6:30 p.m.:

Title: Exploring the Glass Platform

Abstract: By bringing technology closer, we can get it out of the way.  This innovative idea will be taken as a foundation for exploring Glass and the Glass platform.  We’ll cover the latest design principles for Glass software (called Glassware), continue with an overview of the Glass platform, and take an in-depth look at the Google Mirror API.  Examples of current and future Glassware will be shown to demonstrate best practices and give a glimpse at the future of personal computing we are creating together.  Plenty of time will be left for questions and conversation.

Speaker: Jenny Murphy

Jenny is a Staff Developer Programs Engineer on Google Glass. In this role she helps developers use Google APIs and technologies to build cool stuff for Glass. Before joining Google she worked in a wide variety of software engineering roles from robotics at NASA to the architect of a social media startup. She is passionate about writing and education, especially on the subjects of technology and science.

 

APM Talk – 4:30-5:30 p.m., CSE403: 

 

Title: APM Info Session

 

Abstract: Come and learn about Google’s Associate Product Manager role from a UW Alumni who’s doing it!

We’ll cover what it is, how to apply and interviewing tips!

Speaker: Allyson Gale

October 1, 2013

Two upcoming talks – ugrads invited

Reminder about postings, you can sign up to receive notices of talks given in the department by going to: http://www.cs.washington.edu/events/colloquia/

You can also sign into your ugrad-news account profile and determine which categories you receive.

Here are a few talks coming up:

This Thursday – please join us if you can or watch remotely at
http://www.cs.washington.edu/events/colloq_info/

UNIVERSITY OF WASHINGTON
Computer Science and Engineering
*DISTINGUISHED LECTURE*

SPEAKER:   David Patterson, UC Berkeley

TITLE:     Myths about MOOCs, Ebooks, and Software Engineering Education

DATE:      Thursday, September 26, 2013
TIME:      3:30pm
PLACE:     EEB-105
HOST:      Ed Lazowska

ABSTRACT:

This talk explains how the confluence of cloud computing and Massive Open
Online Courses (MOOCs) have allowed us greatly improve both the
effectiveness and the reach of UC Berkeley’s undergraduate software
engineering course.

The first part of the talk is motivated by Industry’s long-standing
complaint that academia ignores vital software topics, leaving students
unprepared upon graduation. Traditional approaches to software development
are neither supported by tools that students could readily use, nor
appropriate for projects whose scope matched a college course. Hence,
instructors traditionally lecture about software engineering topics, while
students continue to build software more or less the way they always had,
in practice relegating software engineering to little more than a project
course. This sad but stable state of affairs is frustrating to
instructors, boring to students, and disappointing to industry.

Happily, cloud computing and the shift in the software industry towards
software as a service has led to highly-productive tools and techniques
that are a much better match to the classroom than earlier software
development methods. That is, not only has the future of software been
revolutionized, it has changed in a way that makes it easier to teach.
UC Berkeley’s revised Software Engineering course leverages this
productivity to allow students to both enhance a legacy application and to
develop a new app that matches requirements of non-technical customers. By
experiencing the whole software life cycle repeatedly within a single
college course, students actually use the skills that industry has long
encouraged and learn to appreciate them.  The course is now rewarding for
faculty, popular with students, and praised by industry.

The second part of the talk is about our experience using MOOCs to teach
Software Engineering. While the media’s spotlight on MOOCs continues
unabated, a recent opinion piece expresses grave concerns about their role
(“Will MOOCs Destroy Academia?”, Moshe Vardi, CACM 55(11), Nov. 2012).   I
will try to bust a few MOOC myths by presenting provocative, if anecdotal,
evidence that appropriate use of MOOC technology can improve on-campus
pedagogy, increase student throughput while raising course quality, and
even reinvigorate faculty teaching. I’ll also explain the role of MOOCs in
enabling half-dozen universities to replicate and build upon our work via
Small Private Online Courses (SPOCs) from EdX and our electronic textbook.

I conclude that the 21st century textbook may prove to be a hybrid of
SPOCs and Ebooks.

Work in collaboration with Armando Fox, UC Berkeley.

Bio:
David Patterson joined UC Berkeley in 1977 after receiving all his degrees
from UCLA.

His most successful projects have likely been Reduced Instruction Set
Computers (RISC), Redundant Arrays of Inexpensive Disks (RAID), and
Network of Workstations (NOW). All three projects helped lead to
multibillion-dollar industries. This research led to many papers and six
books, with the most popular book being Computer Organization and Design
co-authored with John Hennessy and the most recent being Engineering
Software as a Service co-authored with Armando Fox. His current research
is centered on cancer genomics for the AMP and ASPIRE Labs.

In the past, he served as Director of the Parallel Computing Lab, Director
of the Reliable And Distributed Systems Lab, Chair of Berkeley’s CS
Division, Chair of the Computing Research Association (CRA), and President
of the Association for Computing Machinery (ACM).
This work resulted in 35 honors, some shared with friends. His research
awards include election to the National Academy of Engineering, the
National Academy of Sciences, and the Silicon Valley Engineering Hall of
Fame along with being named Fellow of the Computer History Museum, ACM,
IEEE, and both AAAS organizations. He received Distinguished Service
Awards from ACM, CRA, and SIGARCH. His teaching honors include the ACM
Karlstrom Outstanding Educator Award, the IEEE Mulligan Education Medal,
the IEEE Undergraduate Teaching Award, and the UC Berkeley Distinguished
Teaching Award.
Refreshments to be served in room prior to talk.

*NOTE* This lecture will be broadcast live via the Internet. See
http://www.cs.washington.edu/news/colloq.info.html for more information.

Email: talk-info@cs.washington.edu
Info: http://www.cs.washington.edu/
(206) 543-1695

The University of Washington is committed to providing access, equal
opportunity and reasonable accomodation in its services, programs,
activities, education and employment for individuals with disabilities.
To request disability accommodation, contact the Disability Services
Office at least ten days in advance of the event at: (206) 543-6450/V,
(206) 543-6452/TTY, (206) 685-7264 (FAX), or email at
dso@u.washington.edu.

 

____________________________________________

Hello,

Please join the eScience Institute Monday, September 30, 4:00 pm in EEB-303.  Refreshments will be provided.

Orly Alter (Utah):

Orly Alter, Ph.D. is a USTAR Associate Professor of Bioengineering and Human Genetics at the Scientific Computing and Imaging (SCI) Institute at the University of Utah. She was awarded a National Science Foundation CAREER Award in 2009, and a National Human Genome Research Institute (NHGRI) R01 grant in 2007. She was selected to give the Linear Algebra and its Applications Lecture of the International Linear Algebra Society in 2005, and received an NHGRI Individual Mentored Research Scientist Development Award in Genomic Research and Analysis in 2000, and a Sloan Foundation/Department of Energy Postdoctoral Fellowship in Computational Molecular Biology in 1999. Additional support for her work comes from the Utah Science, Technology and Research (USTAR) Initiative.

Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data

In my Genomic Signal Processing Lab, we are breaking new ground in mathematics, at the interface of mathematics, biology and medicine, and in biology and medicine. In mathematics, we develop generalizations of the mathematical frameworks that underlie the theoretical description of the physical world [1].  At the interface, we use these frameworks to create models that compare and integrate different types of large-scale molecular biological data.  In biology and medicine, we use the models to computationally predict previously unknown physical, cellular and evolutionary mechanisms that govern the activity of DNA and RNA.  We believe that future discovery and control in biology and medicine will come from the mathematical modeling of large-scale molecular biological data, just as Kepler discovered the laws of planetary motion by using mathematics to describe trends in astronomical data [2].

At the interface, our recent generalized singular value decomposition (GSVD) comparison of two patient-matched genomic datasets uncovered a global pattern of DNA aberrations that is correlated with, and possibly causally related to, brain cancer survival [3].  This new link between a glioblastoma multiforme (GBM) tumor’s genome and a patient’s prognosis offers insights into the cancer’s formation and growth, and suggests promising drug targets. The best prognostic predictor of GBM prior to this discovery was the patient’s age at diagnosis.  In mathematics, the higher-order GSVD we formulated is the only framework to date that enables comparison of more than two patient-matched but probe-independent datasets, and, in general, more than two datasets arranged in matrices of the same column dimensions but different row dimensions [4].  In biology, our experiments [5] verified our prediction [6] of a global causal coordination between DNA replication origin activity and mRNA expression, demonstrating that matrix and tensor modeling of DNA microarray data [7] can be used to correctly predict previously unknown biological modes of regulation.  Ultimately we hope to bring physicians a step closer to one day being able to predict and control the progression of cell division and cancer as readily as NASA engineers plot the trajectories of spacecraft today.

September 25, 2013

Meet tech leaders at the GeekWire Summit 2013

Where can you hear from a renowned Silicon Valley venture capitalist, the leader of Microsoft’s Halo business, HBO’s top technology executive, the former Nordstrom.com president, and an Amazon veteran aiming to upend traditional retail with the help of robots?

It’s the GeekWire Summit, our biggest event of the year, coming up on Sept. 12 in Seattle. Today we’re sharing exclusive details about this one-of-a-kind technology conference with you, as a past attendee of GeekWire events.

Tickets for the Summit are available here!

+ Here’s a promo code for 10% off for UWCSE: Use code CSE10Summit

Newly added to the GeekWire Summit agenda is Bill Gurley, known as one of “technology’s top dealmakers” as a general partner at the Benchmark venture capital firm. Gurley, a Zillow board member, will join technology vet Rich Barton, the Expedia and Zillow co-founder, for an on-stage conversation about key trends to watch in technology, investing, startups and more.

We’re also pleased to welcome Bonnie Ross, who oversees the blockbuster Halo business as the general manager of Microsoft’s 343 Industries. Ross will be one of the participants in a panel on the future of video games, moderated by game industry veteran and adviser Ed Fries.

A panel on the future of retail — featuring veterans of Amazon, Starbucks and Nordstrom — will examine the changing nature of e-commerce and the increasing crossover between the physical and digital worlds. Panelists include Jane Park, the CEO of cosmetics e-commerce startup Julep; Dr. Nadia Shouraboura, the CEO of robot-powered apparel startup Hointer; and Michael Smith, the CEO of organic food delivery service Full Circle Farms, and former president of Nordstrom.com

HBO’s Otto Berkes, the Microsoft Xbox and tablet computing veteran who is now the chief technology officer of HBO, will share his insights into the evolving world of digital media and devices. HBO is one of many companies that have opened engineering offices in the Seattle region, giving Berkes an additional perspective on the technology climate.

Chase Jarvis, the visionary photographer, director, and fine artist who founded fast-growing online education startup creativeLive, will offer his perspective on the evolving world of digital media and online education.

And a capstone panel on the future of innovation — one of the most popular sessions at last year’s event — will feature industry vets including Jeremy Jaech (of Aldus and Visio fame) who has returned to the startup world as the CEO of home sensor startup SNUPI Technologies, a UW spin-out.

The GeekWire Summit is the premier technology conference in the Pacific Northwest. Organized and curated by GeekWire’s John Cook and Todd Bishop, this event brings together engineers, entrepreneurs and business leaders from around the region and the country for conversations and insights at the intersection of business and technology, reflecting GeekWire’s mission to inform, empower and unite the region’s technology community.

We’re looking forward to seeing you on Sept. 12!

August 21, 2013

Thursday, June 6, 2013 Manageability Systems @Twitter: towards efficiency and reliability

You can always find out about upcoming talks open to all, by going to this webpage: https://www.cs.washington.edu/events/colloquia/

here is one that we thought ugrads might be particularly interested in.

UNIVERSITY OF WASHINGTON
Computer Science & Engineering
TECH TALK

SPEAKER:   Jeff Currier, Twitter

TITLE:     Manageability Systems @Twitter: towards efficiency and
reliability

DATE:      Thursday, June 6, 2013
TIME:      4:30pm
PLACE:     CSE 403

ABSTRACT:
This talk will focus on the manageability systems that Twitter is building
to increase the overall reliability and efficiency of our services.
Further, practical applications of the techniques captured in this
substrate benefit the services that allow Twitter to operate at a massive
scale.

Speaker Bio:
Jeff Currier is a Engineering Manager in Twitter’s Seattle Engineering
office. He’s leading a team who is focused on building technologies that
enable service self healing, automatic load balancing of data systems and
making running services at scale more economical.

June 3, 2013

eScience Institute talks coming up

Hello,

Please join the eScience Institute Wednesday, May 1, 4:00 pm in EEB-303.  Refreshments will be provided. 

Jeff Gardner (UW Physics)

Jeff Gardner is Director of Research for Physical Sciences at the eScience Institute, Affiliate Assistant Professor in the Physics and Astronomy departments, and Visiting Faculty at Google, Inc.  Jeff received his PhD in Astronomy from UW in 2000.  In 2003, he become a Sr. Research Scientist at the Pittsburgh Supercomputing Center, where he participated in the deployment of the NSF TeraGrid (Extensible Terascale Facility; ETF), which became the largest open platform for scientific computing in the world. His research has focused on the overcoming the challenges of analyzing extremely large scientific datasets using a variety of approaches, including scalable DBMSs, MapReduce, as well as domain-specific libraries.  He is also actively involved in building the next generation of computational astrophysics codes capable of sustaining a petaflop (1 thousand trillion mathematical operations per second) and generating petabytes of data.

Simulating the Universe on Google’s Exacycle Platform

The Large Synoptic Survey Telescope (LSST; http://www.lsst.org ) is one of the most ambitious astrophysical research programs ever undertaken.   From the 9,000 ft Cerro Pachon peak in Northern Chile, the LSST’s 3.2 Gigapixel camera will repeatedly survey the southern sky, taking one image every 15 seconds, generating tens of petabytes of data every year.  The images and catalogs from the LSST have the potential to transform both our understanding of the universe and the way that we undertake science.  As part of the implementation phase of this project, the LSST collaboration has undertaken a formidable program to simulate the flow of data from the telescope.  The image simulator traces individual photons of light from stars, galaxies, asteroids, through the earth’s atmosphere, the telescope optics, and onto the detector.  These simulations are used to optimize how the LSST surveys the sky, to develop the analytics required to understand how the universe forms and evolves, and to determine how astronomers (and the public as a whole) will scale science to data sets that will exceed a hundred petabytes in size.  For over a year now, Google has given LSST access to their Exacycle platform in order to perform these simulations (http://research.google.com/university/exacycle_program.html), reducing the time required to simulate one night of LSST observing, roughly 5 million images, from 3 months down to a few days.  This rapid turnaround enables the LSST engineering teams to test new designs and new algorithms with unprecedented precision, which will ultimately lead to bigger and better science.

 

Upcoming Seminars:

* May 13, 4 PM (EE303)

      Fernando Perez  (Berkeley)

               TBD

* May 22, 4 PM (EE303)

      Joe Hellerstein  (Berkeley)

             Why Computer Scientists Should and Can Learn Computer Science

April 25, 2013

Barry Wark, Ph.D (Physion) will be giving a talk on: Challenges in Life Sciences data management and cloud enabled collaboration

Hello,

Please join the eScience Institute Thursday, April 11, 4:00 pm in EEB-303.  Refreshments will be provided.

Barry Wark, Ph.D (Physion) will be giving a talk on:

 

Challenges in Life Sciences data management and cloud enabled collaboration

 

 

Upcoming Seminars:

* May 1, 4 PM (EE303)

Jeff Gardner  (UW)

Simulating the Universe on Google’s Exacycle Platform

* May 13, 4 PM (EE303)

Fernando Perez  (Berkeley)

TBD

 

April 4, 2013

Talks list

If you want to receive emails about the various talks going on in the department, you should subscribe to the talks list.

https://mailman.cs.washington.edu/mailman/listinfo/talks

We generally will not post reminders here, but do towards the beginning of each quarter. Also, remember that you can sign in to the blog to set preferences on the types of message you receive.

Crystal

Information about upcoming Colloquia sponsored by the University of Washington, Department of Computer <talks@cs.washington.edu>
Mar 28 (4 days ago)
to cs-ugrads

Intriguing title on this one…!

UNIVERSITY OF WASHINGTON
Computer Science and Engineering
COLLOQUIUM

SPEAKER:   Shayan Oveis Gharan, Stanford University

TITLE:     New Approximation Algorithms for Traveling Salesman Problem

DATE:      Thursday, April 4, 2013
TIME:      3:30pm
PLACE:     EEB-105
HOST:      Anup Rao

ABSTRACT:
TSP is a central and perhaps one of the most well-known problems in
theoretical computer science. Due to its combination of simplicity, appeal
to imagination, and intractability, TSP has attracted the attention of
mathematicians and computer scientists for decades. Despite this
attention, the best approximation algorithm known for TSP goes back to
1976. In his unpublished manuscript, Christofides presented a simple
3/2-approximation algorithm for the problem.

In a joint work with Saberi and Singh, we design a new approximation
algorithm for a canonical special case of the TSP known as graphic TSP.
This algorithm finally breaks the 3/2 barrier by a very small constant.
Our algorithm employs a new technique for rounding the optimum fractional
solution of linear programming relaxations of combinatorial optimization
problems, called the rounding by sampling method.  Our analysis builds on
recent developments in probability theory on properties of strongly
Rayleigh measures, as well as new insights from combinatorics and
polyhedral theory. As a byproduct of our result, we show new properties of
near minimum cuts of any graph, which may be of independent interest.

Bio:
Shayan Oveis Gharan is currently finishing his PhD at Stanford University
under the supervision of Amin Saberi. Prior to Stanford, Shayan received a
BA in computer engineering from Sharif University of Technology. His
research interests include Approximation Algorithms, Spectral Algorithms,
Online Algorithms and Applied Probability. He is a recipient of several
awards including best paper award at SODA 2010 and FOCS 2011 for his works
on the Traveling Salesman Problem, Stanford Graduate Fellowship, and the
Miller Fellowship.

Refreshments to be served in room prior to talk.

*NOTE* This lecture will be broadcast live via the Internet. See
http://www.cs.washington.edu/news/colloq.info.html for more information.

Email: talk-info@cs.washington.edu
Info: http://www.cs.washington.edu/
(206) 543-1695

The University of Washington is committed to providing access, equal
opportunity and reasonable accomodation in its services, programs,
activities, education and employment for individuals with disabilities.
To request disability accommodation, contact the Disability Services
Office at least ten days in advance of the event at: (206) 543-6450/V,
(206) 543-6452/TTY, (206) 685-7264 (FAX), or email at
dso@u.washington.edu.
______________________________

April 1, 2013

Special Invitation – Microsoft Webinar – Machine Learning, NLP, and AI

Hello!

We would like to invite you and your students to our next webinar highlighting Machine Learning, Natural Language Process, and Artificial Intelligence. This webinar will feature a presentation by two Microsoft employees solving the complex problems in search. Learn about what recent college hires are working on, as well as how Microsoft is approaching the world of search on a daily basis. By tuning in live, you will have the opportunity to ask questions and interact with our presenters in real-time.

Upcoming Webinar – “Be Smarter Than Your Computer: Machine Learning, Natural Language Processing & Artificial Intelligence”

Wednesday, March 13th @ 12:00 PM (PST)

Register to attend at http://bit.ly/URwebinarAI1

Thursday, March 21st @ 6:00 PM (PST)

Register to attend at http://bit.ly/URwebinarAI2

Do I need to call in to get audio?  Yes, because of the high volume of callers and varying internet connections we have found it is more reliable to call in for audio.  Toll Number: 213-416-1560

Access Code: 240-746-226.  International call in recommendations are listed in the attached flyer.

Are you calling in internationally? If so, we recommend VOIP so you can access the audio. If you’re using a landline, cell phone, Skype, Nonoh, or a similar program, please make sure to dial 00-1 before dialing the number above. If you continue to have problems signing in, please note that we will be posting these webinars online here!

March 12, 2013

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