Friday, September 20, 2013

On Campus Interviews with the CIA 10/25

eScience Seminar with Orly Alter (Utah); Monday, September 30th, 4:00 PM, EEB-303

Please join the eScience Institute on 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.

FLAS Fellowships for undergraduate, graduate and professional students

Foreign Language & Area Studies Fellowships (FLAS) available to undergraduate, graduate and professional students 
Receive tuition and a living stipend: 
        Academic Year Graduate:                  $18,000 tuition, $15,000 living stipend 
           Academic Year Undergraduate:         $10,000 tuition, $5,000 living stipend
           Summer Graduate/Undergraduate:        $5,000 tuition, $2,500 living stipend
The FLAS Fellowship is available to U.S. citizens and permanent residents.  FLAS Fellowships support study of the following languages and their world regions:
 -Arabic –Bangla -Bosnian/Croatian/Serbian –Bulgarian –Burmese -Canadian First Nations –Chinese –Czech –Danish -Estonian -Filipino/Tagalog –Finnish –French –German –Hebrew –Hindi -Indonesian/Malay –Italian –Japanese –Kazakh –Khmer –Korean –Latvian –Lithuanian –Norwegian –Persian –Polish –Portuguese –Russian –Slovenian –Spanish –Swahili –Swedish –Tajik –Thai –Turkish –Uighur –Urdu –Uzbek –Vietnamese
 FLAS Information Sessions, covering FLAS benefits and requirements, the application process, and the use of FLAS awards abroad, will be held at the following dates and times: 
  • Undergraduate Fellowship Fair, Oct 10, 10-2,Mary Gates Hall, FLAS Session 11:30-12:20 MGH 206
  • Study Abroad Fair, Wed, Oct 23, 10-2, Mary Gates Hall, FLAS Session 10:30-11 MGH 258
  • Thomson 317: T Oct 29, 3:30-4:30/ Wed Nov 6, 2:30-3:30/ T Nov 26, 2:30-3:30
  • Denny 213: Wed Nov 13, 3:30-4:30
  • UW Bothell 1-103, Nov 14, 3:30-5
  • Parrington 313: Wed Dec 4, 2:30-3:30

    Applications due January 15, 2014.  Questions: email
    For more information, visit 

Thursday, September 19, 2013

Welcome Back! Forum on Science, Ethics, and Policy (FOSEP) Student Group

Welcome back new and continuing students, staff, and faculty to the University of Washington!

Science affects nearly every aspect of American policy. Several major challenges faced by society have solutions that are based on science, yet there is little emphasis to educate scientists in training about policy and communication. To improve the impression of science in culture and the support of scientific research among taxpayers and policy makers, scientists must engage in effective communication and participate in policy discussions.

The *Forum on Science, Ethics, and Policy (FOSEP)* at the University of Washington is a group of dedicated undergraduate, graduate, and post-doctoral fellows who are concerned about a range of issues that surround the practice and funding of research. We believe FOSEP can successfully educate its student members about the intersection of science and society in a way that is not accessible within a traditional graduate education. With this mission, FOSEP is training the citizen scientists of the future.

*More information* regarding FOSEP can be found at:

*If interested in joining* FOSEP, please complete this short (very short) catalyst survey at Responsibilities of general FOSEP members are negligible, but we do hope that you will attend FOSEP events and spread the word about FOSEP in your department.

*Please join us on October 8th at 5pm for an introduction to FOSEP * and a lively discussion of the way scientific research, and specifically health information, is communicated. We will be looking at conflicting reports about the health effects of caffeine. With conflicting reports seemingly presented every week by scientists, does the public gain or lose trust in science as an institution? Refreshments will be provided. Please *RSVP to*.

2014 Cornell Cup USA presented by Intel Competition

Space Available in CSE 467 for EE Majors

We will have 5 spaces open for EE majors who want to take 467 this fall.  The prerequisites for them will be : EE 271 and EE 478.
If interested, they should email the instructor:  Gabe Cohn <> for an add code.  Here is a description of the course: 

CSE467: Advanced Digital Design – Gabriel Cohn
How you ever wondered how the Xbox Kinect and other computer vision systems can compute complicated algorithms on large data sets in real-time? Take CSE 467 to learn how to dramatically accelerate an algorithm by implementing it on custom hardware! Such hardware acceleration is commonly used for high speed computations in computer vision, artificial intelligence, computational biology, and finance. The class project will allow students to implement a highly optimized computer vision algorithm on an FGPA.

Wednesday, September 18, 2013

Undergraduate Research Opportunities in EE

I am looking to hire hourly student research assistants for the fall quarter for three different projects.

1) Automatic speech recognition for low-resource languages: Current speech recognition technology relies on machine learning methods that leverage large amounts of transcribed data.  In this project, we are interested in languages other than English, in which case there may not be a lot of data available.  This project will involve harvesting data from the web for augmenting small data sets and learning methods that account for style differences.

2) Automatic detection and classification of marine mammals: Detection of marine mammals is important for avoiding sonar operations when they are present and for tracking populations.  The problem is challenging because of the highly variable noise conditions in the oceans. We have developed some prototype algorithms in Matlab and are looking for someone to work on porting these algorithms to C/C++ and factoring the implementation to leverage parallel processing and allow experimentation with large amounts of data. Once the software is in place, the goal is to explore semi-supervised learning algorithms.

3) Speaking style analysis: Spoken language carries much more information than one can see in the transcript, including emotion, strength of belief, sarcasm, etc.  In this project, we investigate signal processing methods to extract cues that an automatic system could use to recognize this information.

All projects will require computer implementation of algorithms for data processing and analysis. 

Computer programming skills and experience, including: experience with unix, programming languages such as C, C++ or Java and scripting languages such as Perl or Python. Students should have completed and done well in both CS142 and 143 (at least). Knowledge of probability is very useful for anticipated work on machine learning. For projects 2 & 3, experience with Matlab is desirable.

Hours & Salary:
The position will involve 10-19 hrs/week, flexible hours, depending on student availability. The salary is $12-15/hr, depending on experience.  

Application Documents:
CV, (unofficial) transcript, and the contact information of one or two references, including either the instructor for one of your programming courses or a supervisor for whom you've done programming.

Interested candidates may send their application material to Prof. Ostendorf at  If you are interested in the first position, please copy Aaron Jaech (, if interested in the second position, please copy Nicole Nichols (, and if interested in the third position, please copy Vicky Zayats (

Tuesday, September 17, 2013

RFID Programming Short-Term Job

Currently we get our RFID tags that we use on some supplies that we provide to school districts from China. The RFID tags use the ISO 156393 IC- Code SLI protocol. I do have the information that gets written into the RFID blocks (which are subsequently locked) and the other blocks are left unwritten, the machines that use our supplies write code on it. I have some equipment here at our Warehouse in Renton. It should not take more than 2 hours of your time. I am willing to pay $100/hr. I can give you pictures and more information of the tags once you find a proper candidate. The tags use NPX chips.
Let me know.

Francis S Whelan
Witt Company
850 SW 7th Street Suite 100
Renton, WA 98057

Monday, September 16, 2013

Join the Dream Project - 2-credit service-learning opportunity

We'd like to invite you to join the University of Washington Dream Project! It's the mission of the UW Dream Project to assist low-income and first-generation high school students in attaining higher education and to raise awareness among university students about the issues of educational opportunity and social mobility. 

We would love to have you join us this fall as we dive right into working with the senior high school students as they are writing essays, completing college applications, preparing for the SAT/Act and applying for scholarships.  In the words of a recent Dream Project mentee who is now a UW freshman, “You never know what conversation with a student is going to totally change their life trajectory.”

What’s in it for you?

• First-hand learning about educational access, mentoring strategies, and social justice.
• 2 credits (1 credit of EDUC 260, lecture; 1 credit of EDUC 369, high school visit)
• I&S credit for EDUC 260, Service Learning (S) credit for both EDUC 260 and 369
• Leadership opportunities ranging from leading lectures to running events for hundreds of people
• Eligibility for PAID part time student jobs as College & Career Readiness Assistants after 3 quarters in the Dream Project
• Transportation to the high schools is included!
• FREE COFFEE every week at the earliest morning visits.
• Writing credit is available. Find out more at

If you don’t want credit, you can have the exact same experience participating on a volunteer basis. For details on how to join, see, email us at or stop by the Dream Project Center in Mary Gates 274. We welcome students of all majors or premajors, freshmen through super-senior, who are interested in becoming mentors.

UW Dream Project

Research Software from Oxford University Scientists

We would like to introduce you to the solution we developed, colwiz – collective wizdom, free software designed to accelerate the pace of innovation and increase overall research productivity.
Using colwiz web, desktop, iPhone, iPad and Android Apps, researchers can:
  • Search publications on Google Scholar, PubMed and 30+ other search engines, automatically find PDFs and take notes, write articles with citations and bibliographies.
  • Make to-do lists, collaborate on research tasks, and schedule journal clubs, conferences and deadlines.
  • Store, backup and share research data and files.
  • Create groups, invite other researchers to collaborate through shared publications, calendars, tasks, documents and discussion areas.
  • Manage multiple research projects across departmental, institutional and geographical boundaries.
  • Organise their research lives, from initial idea, through complex collaborations, to publication of the results.
Colwiz is designed for individual and collaborative research and used by researchers from around the globe. Our website ( and video ( explain how graduate students writing their theses and research groups working on complex collaborative projects will find it equally useful.

ESRM 320, Marketing & Management From a Sustainability Perspective

ESRM 320, Marketing & Management From a Sustainability Perspective
5 credits, NW and I&S credit, SLN 14133
TU/TH 5:30-8 PM
223 Anderson Hall
ABOUT 320...
For-profit companies and non-profit organizations use marketing and human resources to create and deliver products, services, and ideas. This course explores: 1) business practices that are aligned with environmental stewardship and social responsibility standards; 2) the concepts and models of a market orientation; 3) how markets are researched and targeted, and products positioned, to meet consumer needs; 4) creating and pricing products, developing distribution channels, and implementing promotion campaigns; 5) managerial and leadership skills and styles; 6) how companies motivate employees and develop human capital; and 7) methods for recruiting, selecting, training, and evaluating employees.
* What does sustainability mean, and how is it manifested in business? Various definitions of sustainability have been used, but all share a common understanding that sustainability refers to integrating environmental, social responsibility, and financial/economic elements in order to meet the needs of people today without compromising Earth’s capacity to provide for future generations. Said another way, practicing sustainability involves balancing the three Ps: planet, people, and profits.