Introducing the SEFS Shared Genetics Laboratory!

After many months of planning and set-up, room renovations and equipment tweaks, we are very pleased to announce that our new SEFS Shared Genetics Laboratory is fully open and operational in Bloedel 170!

Funded by Professor Laura Prugh, SEFS and a Student Technology Fee grant that alumna Melissa Pingree secured, the newly refurbished lab is designed to focus on non-invasive, low-quality/low-quantity DNA genetic testing from hair, scat, saliva,  water, soil and other collected material that doesn’t require the capture of an animal (though the lab is also capable of handling blood and tissue sampling). It’s equipped with highly specialized technologies, including a droplet digital PCR machine to detect very low levels of DNA, and is open to SEFS graduate and undergraduate students in need of space and equipment for their genetic research, whether they’re exploring bacterial communities in soil, or identifying species through hair samples. While using the equipment is free—dependent on availability—students do have to provide their own supplies.

Several graduate students are already using the lab, including a project that involves swabbing bite marks on killed ungulates to determine predator identification. There’s also a new citizen science project on Vashon Island through the Vashon Nature Center that involves a pilot coyote study to try to isolate quality DNA from scat samples to determine individual identification.

The possibilities range widely, and the best way to see how the lab might support your own research is to contact the lab manager, Kelly Williams. Originally from Upstate New York, Kelly earned a master’s in ecology from Colorado State University, and her graduate research involved developing a method of detecting feral pig DNA in water samples (she just had her paper accepted in PLOS ONE!). In addition to assisting graduate student projects, she is currently training and working with three undergraduate student volunteers this summer to help extract DNA scat samples from Alaska as part of one of Laura’s grants.

If you’d like to learn more about the lab or set up a tour, contact Kelly anytime!

Lab manager Kelly Williams with the PCR workstation.

Field Research Kits Now Available for Students

No matter the remoteness of your field site, and no matter how much icy rain is lashing your face and hands, you can now thumb your nose at the obstacles and elements and carry on bravely—and ever so ably—thanks to an impressive arsenal of equipment available in 10 new field research kits!

Field Kits

SEFS grad students Matthew Aghai (right) and Kiwoong Lee try out the field kits at Cedar River Watershed.

Purchased this past spring through a $30,437.95 grant from the Student Technology Fee (STF), these field kits are designed to make collecting and sharing data in the field immensely more efficient and effective. The kits are available for students to check out and use for free, and they feature a wide range of gear, including iPads with solar keyboards, clinometers, 30-meter Spencer® tapes, digital waterproof calipers, rangefinders, portable power packs, Garmin™ GPS units and other tools to aid research on the go. Five of the kits are more basic, and five are more advanced, and they are all stored in Winkenwerder Hall on the main UW campus.

“They’ve been hugely useful,” says SEFS graduate student Matthew Aghai, who was involved in securing the STF grant and has already put the kits to work this summer.

So who can use them?
The kits are tailored for College of the Environment graduate and undergraduate students conducting field research, but they are open to all students at the University of Washington.

How do you get started?
Whether you’re heading out for a weekend or an entire field season—or even as part of a class with a field component—the kits are available on a first-come, first-served basis. Also, after you’ve examined and decided to check out a kit, make sure to factor in some time to meet with SEFS IT to load the software and apps you’ll need for your research, because you won’t be able to add new programs from the field.

Email Matthew Aghai to learn more and check out a kit!

Photo of kits in action © Emilio Vilanova; photo of opened kit © SEFS.

Field Research Kit

Gibson Virtual Desktops: Mobile Computing, From Anywhere!

Behind the scenes of most technology projects at SEFS—whether in your office, the classroom or out in the field—are a number of resources that help support your research and studies. Among the least visible, yet also the most powerful and versatile of these resources, is our own virtual desktop environment, known as Gibson.

Named for the supercomputer in the movie Hackers, Gibson provides fully secure, 24-hour remote access to high-end software previously available only by visiting SEFS computing labs. The core system is a commercial product, but the SEFS IT Team specifically configured Gibson to meet the needs of classes and research in our school, from remote sensing to data analysis and statistics—all while using only a fraction of the power of a normal computer.

Gibson

Gibson!

Much of the impetus for developing this system, after all, was hearing about students who had to drive or bus a half hour into campus just to run a certain program for five minutes. Now, all of our students can access Gibson’s programs and features anywhere there’s an internet connection. You can even save preferences and data, and when you later log on to the virtual desktop—no matter where you are in the world—you’ll have your personalized computer waiting for you, along with the full suite of SEFS online resources and software at your fingertips.

Gibson, in short, provides the ultimate mobile computing experience. “It’s like having your own personal cloud,” says Shane Krause, senior computer specialist for SEFS.

Launched by Krause about two years ago, the pilot of Gibson was funded by the Student Technology Fee, along with research funds from Professors Stanley Asah and Soo-Hyung Kim, both of whom were looking for a more mobile system to help their students. Since then the system has grown and evolved with a number of infrastructure improvements, including adding faster hardware and recently moving the entire system from Bloedel Hall over to one of the UW’s main datacenters.

Gibson is now available to all SEFS students, faculty and staff, and the system has seen expanded use on campus, including in other units of the College of the Environment, and at remote sites such as the Arboretum, ONRC and Pack Forest. In fact, the system has already served nearly 1,000 unique users, and there’s plenty of room for more, say Krause and Marc Morrison. So jump in there and get connected—Gibson is ready for primetime!

Student Technology Fee Grant Winners for SEFS!

Marc Morrison was very pleased to report that four SEFS proposals—all student-driven—were recently funded by Student Technology Fee (STF) grants!

STF is funded by UW students with a $41 fee assessed each quarter. Every year, in turn, university departments and students can send in requests for grants from this fund to help cover a variety of technological ventures around campus, such as acquiring lab equipment or gear for field research. As the name of the program suggests, these grants must be geared toward student use, and last year STF funded nearly $5 million in projects.

This year, SEFS students helped secure nearly $250,000 in funding, so check out the winning proposals below! (Also, if you’d like to apply for STF funding next year, find out what kinds of projects are eligible.)

2014 Grant Winners for SEFS

Process and Analytical Equipment for Biofuels Production

The Biofuels and Bioproducts Laboratory (BBL) , which explores all aspects of the bioconversion/thermochemical conversion of lignocellulosic materials into biofuels and bioproducts, requested a grant to purchase state-of-the-art analytical tools, including Raman Spectroscopy (RS) as a real-time fermentation measurement technique; GC-MS (Gas chromatography-mass spectrometry) for quantitative product identification; high-pressure syringe pumps for supercritical fluid applications; and powerful, high-speed computers to run simulations to verify and complement experimental results. The computers and process and analytical equipment the lab requested will be a great benefit to not only the BBL graduate and undergraduate students, but to the entire SEFS undergraduate community, because every graduating junior and graduate student in the Bioresource Science & Engineering (BSE) program of SEFS takes BSE 426, which would include experiments to convert ethanol into gasoline using the high-pressure pump, and analysis procedures with the GC-MS and new computers.

Total grant award: $169,909.71

Natural Resources Field Tool Kits
To assist field research capabilities for SEFS graduate and undergraduate students, this grant requested funds to acquire tablet computers with rugged cases and other associated measurement tools, or a “Natural Resources Field Tool Kit” that students can reserve and check out for field-based data collection. The tablets will optimize student information management by allowing direct data input, photography/videography, spatial and mapping inference, as well as access to field guides and scientific literature while in remote settings. The equipment will be available to students campus-wide and will set UW students apart by giving them expertise and opportunities for unexpected innovations using these developing technologies, as opposed to continued reliance on outdated tools and techniques for field research.

Total grant award: $30,437.95

College of the Environment Field Research Equipment
A group of SEFS graduate students requested this grant to purchase wildlife field research equipment that has the potential to benefit many students studying in the College of the Environment. This grant will cover the purchase of remote cameras—currently unavailable to most students—and field equipment to run at least two camera-based wildlife research projects, or provide a College field course with enough equipment to run a thorough wildlife research project. Other items to be purchased, including field laptops, wildlife camera traps, portable GPS units and SPOT receivers (satellite positioning and tracking devices used for emergency communications), will provide students throughout the College with access to state-of-the-art equipment that will allow them to apply what they learn in the classroom to rigorous wildlife field research—including as part of senior capstone projects.

Total grant award: $44,009.62

Restoration Ecology Network GPS Units
The University of Washington Restoration Ecology Network (UW REN) Capstone in Ecological Restoration, a 13-year-old program that continues to grow each year, currently involves 63 students. This grant will allow for the purchase of badly needed equipment—specifically, six GPS units—for ESRM seniors and graduate students to ensure they have the tools to create professional, computer-based maps for their restoration planning documents related to their UW REN Capstone project.

Total grant award: $3,889.05