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2008QuantitativeBiology

Page history last edited by Bryan Schomaker 15 years, 5 months ago

Quantitative Biology II

(Howard Hughes Medical Insitiute, July 21-24, 2008)

 


 

 


 

MEETING OVERVIEW

 

This workshop will bring together mathematics and biology educators who have developed or wish to develop quantitative biology curricula. The major goals of the conference are to:

 

• Identify successful models that introduce applications of and connections with biology into the undergraduate mathematics and computer science curriculum.

• Identify successful models that integrate quantitative methods into biology introductory and upper level courses

• Identify resources and materials that support quantitative biology

• Stimulate creation and revision of new materials that integrate mathematics and biology

• Initiate and foster a collaborative learning community

 

The conference will contain a few invited talks by educators who have been successful in bridging mathematics and biology in the undergraduate curriculum. Most of the sessions will consist of facilitated workshop sessions to identify available resources, address challenges for institutional types, identify gaps in materials and begin planning for a series of meetings and collaborations. Conference participants will consist of collaborative teams of mathematics and biology educators who have plans to pursue such a project at their own institutions. Each team will be asked to submit a brief description of current efforts at their own institution and an outline of their future plans over the next few years. Each team will be asked to bring a poster to the workshop with some details about their current efforts and or future plans.

 

 

 

 


 

AGENDA w/ ABSTRACTS

 


 

 

Monday, July 21

 

3:00-5:00     Registration

 

5:00              Welcome Reception

 

6:00              Dinner   

 

7:15              

OPENING SESSION: WELCOME AND KEYNOTE ADDRESS 

                     HHMI Welcome: Peter Bruns, PhD and Tuajuanda Jordan PhD, HHMI

                     Meeting Agenda: Patricia Marsteller, PhD, Emory University

 

What were the lessons learned from the 2007 meeting and where do we go from here ?  At this working meeting we expect to launch formation of a collaborative community to review and develop interdisciplinary materials and best practices for quantitative biology.  We will review the step initiated and the last meeting and lay out the challenges for this meeting.

 

7:45    

KEYNOTE ADDRESS: MY STUDENTS ARE SMARTER THAN ME!

A. Malcolm Campbell, PhD and Laurie J. Heyer, PhD, Davidson College

Introduced by David Usher, PhD, University of Delaware

 

Today’s students face new pressures from the rapidly changing science and from a globally competitive market. If students only study in their majors, then their options will be limited. Biology has matured to the point where math and computer science are needed to make sense of the vast datasets. If a student seeks a research career, he or she had better pursue an education that enhances his or her quantitative skills. Since our students’ needs are changing, what must we do as their teachers to keep up with the changing demands? How can we retool ourselves and our courses? Do we need new courses? Should we team teach more? Can we tweak what we have and honestly meet the needs of our students? This presentation will offer some answers and invite an honest discussion from the audience.

 

8:45       

Discussion

 

9:00       

Social Hour and Posters

 

 

 


 

Tuesday, July 22  (Posters displayed all day)

 

7:30-8:30     Breakfast

 

8:30-9:30   

KEYNOTE ADDRESS: INTERDISCIPLINARY TRAINING OPPORTUNITIES AT THE NATIONAL SCIENCE FOUNDATION

Mary Ann Horn, Program Director, National Science Foundation, Division of Mathematical Sciences

Introduced by Joseph Watkins, PhD, University of Arizona

 

An overview of some of the training opportunities available at NSF, ranging from undergraduate education to retraining of researchers who are interested in becoming involved in interdisciplinary research will be given.  Examples from successful programs will be used as illustrations.

 

9:30-10:30   

WHITE PAPER 1: Incorporating Biological Problems Into Mathematics Courses

Lester Caudill and Kathy Hoke, University of Richmond

Moderator: Joseph Watkins, PhD, University of Arizona

 

Bio2010, Transforming Undergraduate Education for Future Research Biologists, published in 2003 by the National Research Council, has underscored the need for new and explicit connections between undergraduate mathematics and biology curricula, to train a new generation of future scientists on the power in combining the two. Currently, a small number of schools have attempted to address this need. These efforts generally fall into one of three categories: (i) Incorporating biological problems and examples into existing mathematics courses, (ii) incorporating mathematical techniques into existing biology courses, or (iii) creating new “hybrid” mathematical biology (or biomathematics) courses from scratch. In this presentation, we report on several efforts from both categories (i) and (iii), and identify opportunities for further work.

 

10:30-11:00    Break

 

11:00-12:00   

WHITE PAPER 2: Biology /Mathematics Interdisciplinary Majors and Minors

David C. Usher, PhD and John A. Pelesko, PhD, University of Delaware

Moderator: Katerina Thompson, PhD, University of Maryland

 

Bio2010, Transforming Undergraduate Education for Future Research Biologists, published in 2003 by National Research Council, strongly recommended changing life science curricula to emphasize the physical, chemical and quantitative sciences. The spectrum of approaches towards meeting the goals of Bio2010 ranges from a highly biological to a highly mathematical focus. In the former, new quantitative learning modules are being embedded into biology courses and new biology courses are being developed that emphasize quantitative analysis of biological systems. In the later, mathematicians are being trained to apply their knowledge to biological problems. In this presentation we document the approaches taken at different Universities and Colleges that have produced new interdisciplinary curricula integrating biology and mathematics.

 

12:00-1:30    Lunch

 

1:30-2:30   

WHITE PAPER 3: Incorporating Mathematics Into Biology

Karen Nelson, PhD, University of Maryland, with contributions from Stephan Aley (UTEP), Jeff  Knisley (Eastern Tennessee State University), Bob Kosinski (Clemson University), Jennifer Nelson (Canisius College), and Ethel Stanley (BioQUEST  Beloit College)

Moderator: Ann Findley, PhD, University of Louisiana at Monroe

 

To obtain a deeper understanding of biological phenomena, students need to be immersed in quantitative approaches throughout the biology curriculum. A plethora of materials have been developed to integrate mathematical material into biology courses, but these materials have never been gathered in one place and cataloged.  In fact it seems likely that many mathematically-inclined instructors have found it easier to design their own material rather than wading through what is available online.  While do-it-yourself may be possible for some, many of us are better served by exploring existing resources, choosing one, and modifying it to fit our situation.  Even if we create our own, there is much to be gained by seeing other approaches to the topic.

 

Active members of our committee went though several steps to work out a preliminary database.  The white paper contains a list of resources identified by our committee so far (8 major online series of math/biology modules, miscellaneous modules, and online databases).  We describe the type of information that we believe would be useful to instructors evaluating online resources (such as level, length, and usability), and our preliminary attempts to include these categories in a database.  At the workshop, we plan to ask for input/feedback concerning the usefulness of our evaluation criteria and the completeness of our math and biology keyword list. 

 

2:30-3:30    Panel Discussion of White Papers

Questions and Comments. What else is needed? Should we publish this?

 

3:30-3:45    Break

 

3:45-5:30   

INVITED TALKS: 20 minutes each with discussion at the end

 

BlastEd: An exemplar for Interdisciplinary Learning and Curriculum Development

Randall Pruim, PhD, Calvin College

 

BlastEd is an educational website that explores BLAST (Basic Local Alignment Search Tool), a computational tool for comparing genetic sequences. By providing (1) the relevant background information on genetics and algorithms, and (2) a Java applet that illustrates key elements of the BLAST algorithm, biology students are introduced to important issues in computational thinking and computer science students are introduced to a real-world biological application. Finally, BlastEd provides a model for how to teach natural scientists about computing and how to teach computer scientists about science. The initial work on BlastEd was done in June 2007 during a 1-week workshop jointly sponsored as a Professional Enhancement Program (PREP) of the Mathematical Association of America (MAA), the SC07 Education Program, and the National Computational Science Institute (NCSI). At the workshop mathematics, biology, and computer science educators learned from one another and worked in interdisciplinary teams to produce undergraduate educational materials. In addition to producing version 1 of BlastEd, this project provided valuable insights into both the importance of and the challenges of such interdisciplinary collaborative efforts. Fri, 6/27/08  8:31 AM

 

Mathematical Biology at a Small Undergraduate College: Major, Courses and Research:

Lisette de Pillis, PhD and Steve Adolph, PhD, Harvey Mudd College

 

We will describe our program in mathematical biology at Harvey Mudd College. We established an undergraduate major in mathematical biology in 2002 and our first majors graduated in 2003. Students in this major can choose a variety of electives depending on their interests in mathematics and in biology, and have two academic advisors (one from math, one from bio). Mathematical biology majors have gone on to do a variety of things after they graduate. We teach a capstone course in mathematical biology that is required for these majors and is also taken by students from other majors. This course is co-taught by a mathematician and a biologist, and focuses on modeling. We include diverse biological topics and mathematical approaches. The course also features guest speakers who describe their research. Finally, we will describe some of the faculty and student research projects that involve some combination of mathematics and biology. These projects have involved students and faculty from a variety of disciplines in addition to mathematics and biology. Thu, 6/12/08 4:27 PM

 

Bifurcations in the Ricker model

Bori Mazzag, PhD, Humboldt State University

 

This presentation will illustrate how various mathematical topics are covered in Math 361: Introduction to Mathematical Modeling. This course is taught primarily to upper division mathematics students at Humboldt State University and it focuses on discrete an continuous dynamical systems with applications mainly from biology. I will briefly describe the course content and organization to provide a background, and then show how bifurcations in discrete systems are introduced in this course through a detailed discussion of Ricker's model. The poster will discuss the lecture on this topic and the corresponding two-hour long computer lab. During the lab students use Matlab scripts to answer specific questions, run numerical experiments and explore a given topic (in this case, bifurcations and chaos) in further detail. The talk will close with a summary of successes and limitations of the course in its current format. Mon, 6/9/08 4:47 PM

 

A Freshman Based Approach to Integration of Mathematics, Science and Computation Within a Biological Science Department

James K. Peterson, PhD, Clemson University

 

Since Spring 2006, a calculus course for biologists has been offered at Clemson University which has been taken by 250 students. We have developed the course using the following point of view: 1. All mathematical concepts are tied to real biological need. 2. Mathematics is subordinate to the biology in the sense that the entire course builds the mathematical knowledge needed to study interesting nonlinear biological models. We emphasize that to add more interesting biology requires more difficult mathematics and concomitant intellectual resources. 3. Nonlinear models begin with the logistics equation and progress to Predator - Prey, disease models and a six variable Cancer model. We stress how we must abstract out of biological complexity the variables necessary to build models and how we can be wrong. Our approach is thus replaces second semester engineering calculus with a specially designed course just for biologists and a custom written textbook (www.lulu.com/GneuralGnome). This course is also part of a Quantitative Emphasis minor at Clemson University in Biology and a followup course at the junior level is being prepared and offered in Fall 2008. In this talk, we will frankly discuss the difficulties in 1. choosing our material for this course and why it has been successful. 2. training mathematics colleagues to teach this course. 3. getting two separate deparments to be equally focused on this sort of development. The development of this course is a crucial part in the implementation of concurrent training in mathematics, science and computation within a biological sciences department. We will discuss how we plan to move from our successes with the calculus replacement course to a full integration within the undergraduate degree program that includes long term undergraduate research projects under one professor's direction. We will finish with our plans for the future.

 

5:30-6:00    Refreshments and Personal Time

 

6:00-7:30    Dinner

 

7:30        Posters and Networking

 

 

 


 

July 23rd

 

7:30-8:30     Breakfast

 

8:30-10:30   

CONCURRENT WORKSHOPS

 

Problems and Cases: Integrating Mathematics and Biology

John Pelesko, PhD, University of Delaware and Patricia A. Marsteller, PhD, Emory University

 

Quantitative analysis is an essential tool for 21st century science. The need to develop the quantitative skills of college students, particularly those interested in the biological and biomedical sciences has been the focus of numerous reports since the 90’s. For example, the Bio 2010 report recommends that every biology student learn to apply probability, statistics, discrete mathematics, linear algebra, calculus, and differential equations to the study of biology. On the other hand, pedagogical research suggests that active learning techniques are especially useful in the teaching of science and mathematics. Techniques such as Problem Based Learning (PBL) and Investigative Case Based Learning (ICBL) have proven especially useful in enhancing critical thinking in both biology and mathematics classrooms. In this workshop we will illustrate several examples of PBL units or ICBL cases designed for introductory and advanced biology and introductory and advanced mathematics courses. We will illustrate how these methods can be applied in large and small classes. We will provide resource sites with existing case materials that participants might adopt and adapt. We hope to engage participants in discussions of key biological, mathematical and computational concepts that are now covered by existing materials. Finally, we will establish a working group to develop materials in these key areas. See downloads for powerpoints and handouts.

 

Using Models and Simulations in the classroom from a mathematical biological perspective

Prasad Dhurjati, PhD and Gilberto Schleiniger, PhD, University of Delaware

 

The integration of mathematics and biology in the classroom is illustrated via a practical problem in population dynamics. The concentrations of different species in a bioreactor are tracked. The steps are: 1. Description of the biological system to be studied, and definition of the goals and expectations of the study 2. Mathematical modeling: a. Choice of variables b. Identification of essential features of the system and translation to a mathematical language (a system of differential equations in the population problem to be discussed) c. Identification of the parameters in the mathematical model d. Accounting for the assumptions made in modeling 3. Analysis and simulation of the resulting mathematical model 4. Model validation: Comparison of the predictions obtained from the model with qualitative or quantitative information on the real system 5. Revision of the assumptions and model refinement: Repeat steps 2 – 5. The teaching style we find most appropriate for this kind of integration is a hands on PBL approach. Students are distributed in groups and encouraged to actively work on all steps 1 – 5 above. We will use mathematical analysis, Matlab and Simulink as the tools for solving the equations and simulating the system processes. But, the approach described to integrate biology and mathematics in the classroom is not dependent on the particular tools used to numerically solve the resulting mathematical system.

 

Setting goals and assessing programs and courses

Dave Usher, PhD and Lou Rossi, PhD, University of Delaware

 

In this workshop we will explore programmatic and course assessment to support effective instruction and curriculum design. Assessment is nothing less than the application of rigorous critical thinking and the scientific method applied to instruction. Assessment plays a special role in the development of quantitative concepts, methods and skills used in the biological sciences. Based on department goals, participants will be asked to assess their department needs. In the case of biology and mathematics, the needs may be asymmetric. Biology majors need strong quantitative skills, which must be developed in biology and/or mathematics courses. Math majors need to discover mathematical structure through abstraction of a variety of application domains. Typically, these domains draw heavily from physics and engineering disciplines. However, the life sciences offer an alternative domain for abstraction and discovery of mathematical structure. Participants in this workshop will define goals, develop testable objectives and design assessment tools specific for their own institutions. At the program level, this requires a close relationship between mathematics and biology departments. We will demonstrate the importance of curriculum mapping methods to persuade colleagues to participate in a coherent instructional strategy. However, cross-disciplinary instruction at a large research institution presents unique challenges. Often a learning objective required in one program is taught in courses offered in a different department. As a case study, we will illustrate activities helping biology majors learn calculus at the University of Delaware.

 

Visualization: Learning to See Mathematically via Image Analysis, Networks, Generative Models

John R. Jungck, PhD, Beloit College

 

Compared with Data, and Fractals Images are iconic, symbolic, and memorable.

Thus, most biologists have a rich visual vocabulary and memory. However, most students are not aware that every image if full of data that can be used to test hypotheses. The use of contemporary technology of simple digital cameras for macro and micro-photography lend themselves to extensive use of image analysis. We will draw upon a variety of biological images from different scales to illustrate the power of quantitative, geometric, and topological tools for easy analysis of hypotheses. These have been used with both nonmajor and biology majors. Examples will include: a spatial statistical and graph theoretic polygonal cells in squamous epithelia to detect metastatic clustering (Ka-me’: Voronoi Image Analyzer); network analysis of yeast microarray data to identify metabolic sub-nets (BioGrapher); fractal dimensional analysis of dendritic bacterial colonies grown on hard agar to test self-avoidance searching (Fractal Dimension); image analysis of infected leaves to examine distribution of sites of infection (Image J); , measurements of gastropods used to generate model univalve mollusk (MacRaup); and, measurements of campus trees used to generate a three dimensional model tree which can be examined for such things as miminal self-shading of photosynthesizing laves (3D FractaL Tree – a Lindenmayer system). These are easy activities to include in a variety of biology classes to help provide alternatives to representing everything as a scatterplot or histogram in enabling students to better appreciate the richness of visual data in testing hypotheses. Most of the software demonstrated is freely available through a Creative Commons license through the BioQUEST Curriculum Consortium (www.bioquest.org).

 

10:30-11:00    Break

 

11:00-11:30

Supporting Undergraduate Research Experiences at the Interface of Biology and Mathematics

Discussion led by David Usher, PhD, University of Delaware

 

11:30-12:00   

Disseminating Information

Report on module databases and resources need to maintain this resource (Karen Nelson, PhD, University of Maryland and Ann Findley, PhD, University of Louisiana at Monroe)

Report on a potential University of Arizona repository (Joseph Watkins, PhD, University of Arizona)

 

12:00-1:30    Lunch

 

1:30-3:30    CONCURRENT WORKSHOPS: Earlier sessions repeat

 

3:00-3:30    Break

 

3:30-4:45   

BREAKOUT SESSION: Collecting Resources and Marketing Them to Instructors. 

-What are the best ways to disseminate useful teaching materials?

-How can local efforts be scaled up to a national level? 

[The breakout groups will be based on Carnegie Institutional designation.  

[Institutions PowerPoint]          [Goals PowerPoint]

 

4:45-5:30    Breakout Session Discussion

 

5:30-6:00    Refreshments and Personal Time

 

6:00-7:30    Dinner

 

7:30-9:00    Workshop Discussion

 

9:00        Posters and Networking

 

 


 

July 24th

 

8:00-9:00     Continental Breakfast

 

9:00-10:30   

Implementing Practices that Lead to Institutional Transformation: Faculty Development

Opening remarks and Discussion: Katerina Thompson, PhD, University of Maryland and Joseph Watkins, PhD, University of Arizona

 

Implementing Practices that Lead to Institutional Transformation: Faculty Development Katerina Thompson, University of Maryland and Joe Watkins, University of Arizona Institutions play a critical role in supporting faculty efforts to increase the interdisciplinary emphasis of undergraduate courses and curricula. This session provides some examples of formal and informal institutional mechanisms that facilitate faculty involvement in course and curriculum revision, from professional development to strategies to encourage more interaction between faculty from different disciplines. We will present examples from both research universities and primarily undergraduate institutions. This will be followed by small group breakout discussions in which participants will share examples from their respective institutions, discuss challenges to institutional change, and suggest strategies to facilitate change.

 

10:30-11:00    Break

 

 

11:00-11:45    SUMMARY OF THE MEETING: (Where do we go from here?)

    (Conference organizers)

 

11:45-12:00    CONCLUDING REMARKS: Tuajuanda Jordan, PhD, HHMI

 

12:00     Box Lunch and Departure

 

 


 

DOWNLOADS: TALKS/WORKSHOPS/POSTERS/WHITE PAPERS/RESOURCES

 


 

 

KEYNOTE ADDRESSES:

 

QB I Overview

(Patrica Marsteller, Emory University)

[PowerPoint]

 

My Students are Smarter than Me!

(A. Malcolm Campbell, PhD, Davidson College)

[PDF]

 

Interdisciplinary Research and Training Opportunities at the National Science Foundation

(Mary Ann Horn, National Science Foundation, Division of Mathematical Sciences)

[PowerPoint]

 

 

INVITED TALKS:

 

BlastEd: An exemplar for Interdisciplinary Learning and Curriculum Development

(Randall Pruim, Calvin College)

[PDF]

 

Mathematical Biology at a Small Undergraduate College: Major, Courses and Research:

(Lisette de Pillis, PhD and Steve Adolph, PhD, Harvey Mudd College)

[PowerPoint]

 

Bifurcations in the Ricker Model

(Borbala Mazzag, PhD, Humboldt State University)

 

Why Build a Database?

(Karen Nelson, Ph.D., University of Maryland)

[PDF]

 

A Freshman Based Approach to Integration of Mathematics, Science and Computation Within a Biological Science Department

(James K. Peterson, PhD, Clemson University)

[PowerPoint] and Handouts [PDF]

 

 

WHITE PAPERS:

 

Incorporating Biological Problems into Mathematics Courses

(Lester Caudill, PhD, University of Richmond)

[PowerPoint]

 

Biology/Mathematics Interdisciplinary Approaches: Majors and Minors

(David C. Usher, PhD and John A. Pelesko, PhD, University of Delaware)

[PowerPoint]

 

Incorporating Mathematics into Biology Courses

(Karen Nelson, PhD, University of Maryland)

[PowerPoint]

 

 

WORKSHOPS:

 

Problems and Cases: Integrating Mathematics and Biology

(Patricia Marsteller, PhD, Emory University and John Pelesko, PhD, University of Delaware)

[PowerPoint] [writing cases, ]case, what is pbl

 

Using Models and Simulations in the Classroom from a Mathematical Biological Perspective

(Prasad Dhurjati, PhD, and Gilberto Schleiniger, PhD, University of Delaware)

 

Setting Goals and Assessing Programs and Courses

(David Usher, PhD, and Louis Rossi, PhD, University of Delaware)

 

Visualization: Learning to See Mathematically via Image Analysis, Networks, Generative Models

(John R. Jungck, PhD, Beloit College)

[PDF]

 

 

TALKS and DISCUSSIONS:

 

Supporting undergraduate research experiences at the interface of Biology and Mathematics

(David Usher, University of Delaware and Ann Findley, University of Louisiana Monroe)

[PowerPoint]

 

Disseminating Information: Report on Module Databases and Resources Needed to Maintain Them

(Ann Findley, University of Louisiana Monroe)

[PowerPoint]

 

Report on a Potential University of Arizona Repository

(Joseph Watkins, PhD, University of Arizona)

[PowerPoint]

 

Implementing Practices that Lead to Institutional Transformation: Faculty Development

(Kaci Thompson, University of Maryland and Joe Watkins, University of Arizona)

[PowerPoint]

 

QB II: Where Next?

(Executive Planning Committee)

[PDF]

 

 

POSTERS:

 

Poster Abstracts

          [MS Word]

 

Math and Biology in Trinity University's New Scientific Computing Minor

(Natasa Macura and Mark Brodl, Trinity University)

[PowerPoint]

 

Strategic Planning for Mathematical and Computational Life Sciences

(Pat Marsteller, Emory University)

[PowerPoint , PDF]

 

                    Quantitative Biology at the College of William and Mary

                    (George Gilchrist, College of William and Mary)

                    [PDF] 

 

                    Interdisciplinary Curriculum Reform in the Biological Sciences

                    (Kaci Thompson, University of Maryland) 

                    [PowerPoint]

 

                    Learning Experiences in Integrative Mathematics and Biology

                    at Truman State University

                    (Jason E. Miller and Timothy D. Walston, Truman State University)

                    [PDF]

 

Integrating Biology and Statistics at the freshman level-SYMBIOSIS I:

Biology, a good excuse to talk about probability and statistics

(Edith Seier and Karl Joplin, East Tennessee State University)

[PDF]

 

Integrating Biology and Statistics at the freshman level-SYMBIOSIS I:

Exploring DNA sequences using probability

(Edith Seier and Karl Joplin, East Tennessee State University)

[PDF]

 

Integrating Biology and Statistics at the freshman level-SYMBIOSIS I:

An early introduction to statistical inference

(Edith Seier, Karl Joplin and Jeff Knisley, East Tennessee State University)

[PDF]

 

 


 

PHOTOS

 


 

WORKSHOP PHOTOS:

 

 

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