NIMBioS

NSF Awards $2.9 Million to QUBES: Quantitative Undergraduate Biology Education & Synthesis

Posted on August 27, 2014 by admin

The National Science Foundation’s Division of Undergraduate Education has awarded a five-year, $2.9 million in grants to the project “Supporting Faculty in Quantitative Undergraduate Biology Education and Synthesis (QUBES).” This intiative “addresses the Nation’s growing need to better prepare undergraduate biologists with the quantitative and computational skills needed to be successful in the workplace or in graduate school” and will include the creation of faculty mentoring networks, infrastructure for disseminating resources for teaching quantitative biology, and more. The project is spread out into three separate awards to lead institutions College of William & Mary, the University of Pittsburgh, and the University of Wisconsin-Madison.

The proposal for this grant was born of a “perfect storm” of at least two events from last spring that NIMBioS was involved in. One of the award’s PI Sam Donovan (Biological Sciences, Univ. of Pittsburgh) and co-PI Jeremy Wojdak (Biology, Radford Univ.) were participants in the March 2014 BIO IUSE Ideas Lab, which NIMBioS Director Louis Gross led for NSF. As participants in the Ideas Lab, Donovan and Wojdak were invited to submit a proposal. Later that spring, NIMBioS hosted QUBES Consortium’s first liason meeting in May of 2014 (an RCN-UBE Incubator), at which many parallel needs and possibilities for synergy were explored between interested educational and professional organizations in math and biology such as BioQUEST Curriculum Consortium, the Ecological Society of America, and the Society for Industrial and Applied Mathematics (a complete list of consortium members and PI’s available here). During proposal development, Donovan and Wojdak decided to team up with the existing QUBES initiative to leverage greater impact.

NIMBioS looks forward to being further involved in the future of QUBES, having committed to hosting an advisory board meeting and a faculty development workshop related to the newly awarded grant. Congratulations to the entire grant team that put this idea together that will hopefully benefit the entire undergraduate math and biology education community.

Note: This post corrects an earlier error reporting the award as $1.7 million.

Posted in awards, Education/Outreach, Leadership, STEM | Tagged awards, Education, Education/Outreach, grants, leadership, STEM, teachers | Comments Off

New Textbook Introduces Undergraduates to Mathematics for the Life Sciences

Posted on August 19, 2014 by Catherine Crawley

KNOXVILLE—Today’s students in college biology and other science courses are increasingly being asked to analyze problems in quantitative ways, and now they have a new textbook to help them do so.

“Mathematics for the Life Sciences,” published this month by Princeton Press and co-authored by scientists at the National Institute for Mathematical and Biological Synthesis (NIMBioS), teaches readers about basic mathematical and statistical methods that can be used to explore and explain biological phenomena.

Suitable for entry-level students in biology, agriculture, forestry, wildlife, veterinary science, pre-medicine or pre-health, the textbook introduces readers to the variety of mathematical methods used to create and evaluate models in biology. All that is needed is prior experience with high school algebra, geometry and trigonometry.

The computer tool Matlab and the R language, frequently used in biology, are also introduced to illustrate examples and constructs in basic coding.

The textbook consists of 28 chapters in seven sections—descriptive statistics, discrete time modeling, probability, limits and continuity, derivatives, integration, and differential equations—with exercises at the end of each chapter and suggested student projects at the end of each unit.

“The general aim of the book is to show how mathematics and computational tools can be used effectively to explain problems in the biological sciences that cannot be understand as easily from verbal reasoning alone or from simply analyzing experimental data,” said co-author and NIMBioS Director Louis J. Gross. “The goal is to help readers develop an intuition for the mathematical concepts and techniques discussed in the book so that they can be applied in diverse areas of biology.”

Other authors are NIMBioS Associate Director for Education and Outreach Suzanne Lenhart and Erin N. Bodine, a former NIMBioS graduate research assistant and now an assistant professor of mathematics at Rhodes College.

More information about the textbook as well as complete data files for the textbook exercises can be found athttp://mathematicsforthelifesciences.com/

Citation: Bodine EN, Lenhart S, Gross LJ. 2014. Mathematics for the Life Sciences. Princeton, NJ: Princeton Press. ISBN: 9780691150727

In this video, Dr. Louis Gross and Dr. Suzanne Lenhart describe their new textbook, which aims to assist students in learning about mathematical models used to explore and explain biology.

Posted in books, Education/Outreach, publication, tools | Tagged Education/Outreach, publications | Comments Off

NIMBioS Undergrads Present Summer Research at MBI

Posted on August 19, 2014 by admin

NIMBioS SRE Alumni (L to R) Nitin Krishna, Winode Handagama, Margaret McDaniel and Brittany Boribong take a break from the MBI conference at the Columbus Zoo.

NIMBioS 2014 SRE Alumni (L to R) Nitin Krishna, Winode Handagama, Margaret McDaniel and Brittany Boribong take a break from the MBI conference at the Columbus Zoo.

Our 2014 Summer Research Experience students and teachers may have left NIMBioS for the summer, but friendships forged and research completed carry on! Four NIMBioS SRE undergraduates recently attended the week-long Math Biosciences Institute (MBI) Undergraduate Capstone Conference in Columbus, Ohio. Brittany Boribong, University of Scranton; Nitin Krishna, University of Chicago; Winode Handagama, Maryville College; and Margaret McDaniel, University of Tennessee, all presented their work at the conference.

Boribong said of the experience, “I had a great time at the conference! I really enjoyed it because although people came from different academic backgrounds, everyone had a common interest in how mathematics and biology intersect. It was exciting listening to the student presentations and talking to students at their posters as it allowed me to learn about the type of research that is happening right now in the field of biomathematics. It was great presenting a poster and to see that people were interested in the work my group did this summer. I don’t think anyone that came to my poster knew what a meta-analysis was so it was nice knowing that they all left learning something new. Since I will be a senior in the fall, I also benefited a lot from speaking to representatives from various graduate schools. It helped me feel more at ease about applying to graduate programs.”

Posted in conference, Education/Outreach, research, REU/REV, SRE, undergraduates | Tagged conferences, Education, Education/Outreach, research, REU/REV, SRE, undergraduates | Comments Off

Calling All Nationally Distinguished Biologists

Posted on August 8, 2014 by Catherine Crawley

AIBS Distinguished Scientists Joe Felsenstein (left) and Louis Gross (right)

It’s not everyday that two alumni from the same high school learn that they are both nationally distinguished scientists.

NIMBioS Director Louis Gross and Joe Felsenstein, visiting NIMBioS this week as co-organizer of the Evolutionary Quantitative Genetics Tutorial, both graduated from Central High School in Philadelphia, going back a few decades now.

But they recently discovered that they are both recipients of the Distinguished Scientist award from the American Institute of Biological Sciences, Gross in 2006 and Felsenstein in 2009. The award is presented annually to individuals who have made significant scientific contributions to the field.

Dr. Felsenstein is a professor of genome sciences and biology at the Univ. of Washington, where he has been for more than 40 years. He is best known for his work on statistical inference of phylogenies.

Dr. Gross is, of course, NIMBioS’ fearless leader and at UT, the James R. Cox and Alvin and Sally Beaman Distinguished Professor of Ecology and Evolutionary Biology and Mathematics. He also directs The Institute for Environmental Modeling.

The second-oldest continuously public high school in the country, Central consistently ranks as one of the nation’s top public schools.

Dr. Gross and Dr. Felsenstein are among notable alumni from the school, including two brothers from the Guggenheim family, the popular physician Andrew Weil, and even Larry (Fine) of the Three Stooges.

Congratulations to both Dr. Gross and Dr. Felsenstein!

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Summer Research Students Present Their Findings

Posted on August 1, 2014 by Catherine Crawley

A little audience participation during the final presentation of the Facial Expressions project.

The 2014 Summer Research Experiences for Undergraduates and Teachers drew to a close today with the six project teams presenting their final results.

Margaret McDaniel of the Univ. of Tennessee presents as a part of her team project on Johnne’s Disease

Several groups announced plans to continue their work beyond the SRE program, hoping to continue collaborating with their mentors to prepare manuscripts for publication. Others have already been accepted or made plans to present their work at the MBI Capstone Conference, the SACNAS annual conference, and also the NIMBioS Undergraduate Research Conference at the Interface of Mathematics and Biology, which is now accepting applications to request funding (Deadline: Sept. 10).

At the final luncheon, participants exchanged hugs, words of thanks, farewells and made promises to keep in touch on Facebook or see each other at future conferences.

One participant said he couldn’t think of a better way to have spent his summer than his experience at NIMBioS.

NIMBioS’ highly competitive program accepted 18 students and two high school teachers from around the country. Several of the teams also gained some media experience along the way when they were interviewed about their research on local television and in the local newspaper.

The full set of photos can be viewed here.

Posted in SRE | Tagged REU/REV | Comments Off

Summer Research STEM Symposium Largest Ever

Posted on July 25, 2014 by admin

NIMBioS SRE's Fanguyan Hong, Michelle Cruz, Brittany Boribong and Nikki Rooks amid posters at the STEM Symposium

(From left:) NIMBioS SRE’s Fangyuan Hong, Michelle Cruz, Brittany Boribong and Nikki Rooks at STEM Symposium Poster Session

Last week’s STEM Symposium for undergraduates, teachers and young scholars conducting summer research at the University of Tennessee featured a total of 53 projects, an all-time high for the event now in its third year. NIMBioS collaborates with three other NSF-supported research centers (CURENT, TNSCORE and NICS) on the UT campus to showcase the work of participants in their summer research programs. The result is a large combined poster session where students get to see and share their work with peers and the campus community. Many UT faculty showed up to encourage and recruit students for graduate programs or undergraduate jobs in their labs.

NIMBioS SRE‘s presented in groups on their six different summer projects. For some, it was the first time they had ever created a research poster and their excitement was visible when the posters arrived from the printer. The SRE continues, wrapping up Aug. 1 with student oral presentations at NIMBioS.

Some of the Symposium’s excitement was captured in this video from UT’s Office of Research.

Posted in Education/Outreach, high school, SRE, Teachers, undergraduates | Tagged Education, Education/Outreach, SRE, symposium, teachers | Comments Off

SRE Undergrads In Media Spotlight

Posted on July 23, 2014 by Catherine Crawley

Kelly Moran on camera

Ben Roberson on camera

Marina Massaro on camera

(Updated: Aug. 1, 2014) Research examining facial expression of emotion and research examining the social complexity of Argentine ants — both projects of NIMBioS’ Summer Research Experiences program, were featured in the news recently, and the undergrads working on the projects had the full media experience.

Marina Massaro (Mathematics, SUNY Geneseo); Kelly Moran (Mathematics, Clemson Univ.); and Ben Roberson (Computer Science, UT-Knoxville) were each interviewed on camera, as were their project mentors, psychology professor Jeff Larsen and math professor Chuck Collins, for the facial expressions project.

All three local television news stations as well as the Knoxville News Sentinel attended the event held at Larsen’s pscyhology lab where reporters were able to view how computer software interprets someone’s facial expression while watching different films.

The goal of the project is to better understand how positive and negative emotions, and particularly mixed emotions, are expressed on the face. Understanding how emotions work helps us better understand the nature of human experience. In addition,

Students on the Argentine ant project on camera

answering questions about how people without psychiatric illness experience emotion can help us better understand emotional dysfunction associated with psychiatric illnesses including depression, bipolar disorder and schizophrenia.

The project was covered widely in local media. The print and broadcast stories included the following:

http://www.wbir.com/story/news/local/downtown-ut/2014/07/22/study-looks-into-different-facial-expressions/13014699/

http://www.wate.com/story/26082443/ut-research-students-studying-the-face-of-mixed-emotion

http://www.knoxnews.com/news/local-news/just-an-expression-ut-professors-lead-facial-analysis-project_54608709

The Argentine ant project was also featured in local media. Nicole Rooks (Mathematics, Univ. of Tennessee, Chattanooga), John Marken (Mathematics, College of William & Mary), Brian Whyte (Ecology, SUNY Plattsburgh) along with their mentors, Keenan Mack and Matt Zefferman, were interviewed.

The research seeks to develop an agent-based model to explore how, where and over what timeframe large-scale cooperation within an Argentine ant supercolony could break down.

The following link takes you to media coverage on the local CBS affiliate, WBIR:

http://www.wbir.com/story/news/local/2014/07/29/nimbios-students-study-aggressive-ants-at-ut/13339467/

Posted in SRE, undergraduates | Tagged REU/REV, undergraduates | Comments Off

Girls in Science Campers Quantify Smokies Stream Biodiversity

Posted on July 23, 2014 by admin

Tremont Girls in Science Campers tabulate their data on a dry erase board.

For the fifth year, the NIMBioS Education and Outreach Team headed to the Great Smoky Mountains Institute at Tremont in June to help Girls in Science campers analyze stream biodiversity data using mathematical biology concepts.

During the week-long resident camp, the 24 girls, ages 12 to 15, worked in teams to collect data from two stream locations in the Smokies on type and the abundance of salamanders and stream invertebrates. Beforehand, the girls formed hypotheses for comparing biodiversity in the different streams. On the final day of the camp, Associate Director for Education & Outreach Suzanne Lenhart and Education & Outreach Coordinator Kelly Sturner taught the girls about the exciting world of mathematical biology and how to analyze and interpret their collected data using Simpson’s Index of Biodiversity.

Girls work in teams to analyze their biodiversity data.

NIMBioS returns to Tremont every year to help, but this year’s camp was particularly exciting. One innovation was that the girls had been working on research projects of their own design that lasted throughout the week, working as real young scientists. The other was the greater age range of the students: 12 to 15, instead of 12 and 13 year olds, which made for a more exciting dynamic where the older girls assisted their younger teammates. “I love math!” exclaimed one participant, giving Sturner a high-five. A heart-warming card arrived in the mail at NIMBioS a week later, signed by all the girls, who wrote, “Thank you for teaching us how to analyze our data!”

A second camp takes place July 28-Aug 2, and there may still be room! Contact Tremont today to inquire and sign up your girl, or keep it in mind for next summer.

Posted in Education/Outreach, Middle School, STEM | Tagged Education/Outreach, STEM | Comments Off

Middle School Girls Have STEM Adventures!

Posted on July 2, 2014 by admin

Amy Elliott (center, red shirt) shows the girls a 3D printer that's large enough to print a human-sized chair.

Amy Elliott (center) shows the girls a 3D printer that’s large enough to print a human-sized chair.

In elementary school, 74 percent of girls say they are interested in math and science classes, but women make up only 26 percent of the STEM workforce. Finding ways to retain girls’ interest in STEM to close this gap is the reason why NIMBioS and CURENT collaborated to bring 25 middle school girls from around the region to last week’s Adventures in STEM day camp.

Now in its third year, the camp is a collaborative effort by two NSF-supported research centers at the University of Tennessee interested in promoting diversity in the STEM workforce. In one activity organized by NIMBioS, the girls learned about the biomedical applications of 3D printing, then designed their own 3D models of organisms using Tinkercad that were printed by a Makerbot Replicator 2 for the girls to take home. In another, the girls explored world health data using the dramatic data visualization software Gapminder, and an SIR disease model where the girls simulated an outbreak of fictional “handshake disease.” CURENT, an engineering research center at UT, led activities to help the girls build solar panels and a model neighborhood power grid.

Rising 7th grader Carly Slough plays a spinner game to learn about probability and transitivity.

A highlight of the week was field trip day, when the girls visited Oak Ridge National Laboratory’s Manufacturing Demonstration Facility (MDF) to see the world’s largest 3D printer as well as many other 3D printers that print metals and more. The tours were all led by inspiring female engineers, including Amy Elliott, graduate researcher at MDF and star of Discovery Channel’s 2013 “Big Brain Theory.” Elliott told the girls that when she received second place on the show, she got a sympathetic hug from astronaut Buzz Aldrin who related to her plight as a runner-up. Her current research at ORNL aims to improve 3D printing methods.

Elizabeth Hobson is interviewed by girls about her life and career.

The girls interview Elizabeth Hobson (far left) about her life and science career.

The camp owes its success to numerous volunteers donating their time, including several from NIMBioS. New NIMBioS Graduate Research Assistant Ben Levy, a doctoral student studying mathematical ecology at UT, helped with the camp. In addition, the girls interviewed NIMBioS Postdoctoral Fellow Elizabeth Hobson and Senior Analyst/Webmaster Jane Comiskey about their STEM careers.

More information on initiatives to get girls into STEM from TIME magazine

Posted in Diversity, Education/Outreach, gender diversity, GRAs, Middle School, postdocs, STEM | Tagged careers, diversity, Education, Education/Outreach, GRAs, postdocs, STEM | Comments Off

NIMBioS, UT researchers publish in top journal

Posted on June 25, 2014 by Catherine Crawley

A study on marine viruses and their implication for marine biogeochemical cycles by a group of NIMBioS- and UT-associated researchers has been published in the journal Nature Reviews Microbiology.

The researchers used a biophysical scaling model of intact virus particles to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. They proposed that, under certain circumstances, marine virus populations could make a previously unrecognized and important contribution to the reservoir and cycling of oceanic phosphorus.

The analyses enable quantitative predictions about the elemental content of virus particles of different sizes and could be useful in evaluating the quantitative role that marine viruses play in the storage and recycling of dissolved organic carbon, nitrogen, and phosphorus. According to the study, viruses are predicted to be enriched in phosphorus to such a degree that the total phosphorus content in a burst of released viruses may approach that of the phosphorus content in an uninfected host.

The particle-scale estimates can be extrapolated to ecosystem scales using marine virus survey data. In addition, the researchers hypothesize that the findings could be applied to marine viruses in general, not just virus particles.

The team included scientists from the NIMBioS Working Group on Ocean Viral Dynamics, including Working Group Co-organizer Joshua Weitz, an associate professor biology at the Georgia Institute of Technology, as well as NIMBioS Visiting Graduate Student Fellow Luis Jover, NIMBioS Associate Director for Graduate Education Alison Buchan, UT Professor of Microbiology Steven Wilhelm and T. Chad Effler, a UT undergraduate student in electrical engineering and computer science.

Citation: Jover LF, Effler TC, Buchan A, Wilhelm SW, Weitz JS. 2014. The elemental composition of virus particles: Implications for marine biogeochemical cycles. Nature Reviews Microbiology, 12: 519-528.

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