Truman's Mathematical Biology Program

Jason Miller, John Beck, Michael Kelrick, and Jeffrey Osborn

Truman State University

Research-focused Learning Communities in Mathematical Biology

19 July 2005ECMTB05

Outline

• program goals

• our teams & our learning community

• programmatic activities (summer & other)

• what hasn’t worked and what has

Our Program

Our Program

• use team mentored interdisciplinary research projects as pedagogical vehicle

Our Program


• undergraduates are collaborators

Our Program



• projects are long-term so that students experience the whole range of the scientific enterprise

Our Program



• projects are long-term so that students experience the whole range of the scientific enterprise

• made possible through NSF support (UBM)

Program Goals

Program Goals• to support high quality interdisciplinary research

projects for undergraduates and faculty



• to engage students in activities designed to foster critical thinking skills, intellectual independence and professional and social interaction within the cross-disciplinary student cohort




• to create resources for and to promote the integration of research and teaching in mathematics and biology




• to create resources for and to promote the integration of research and teaching in mathematics and biology

• create and sustain a learning-community with mathematical biology as a common interest

Research Goals

• students are deeply invested and engaged in their project

Research Goals


• students are steeped in both disciplines

Research Goals



• work is peer reviewed and presented at national meetings, published

Research Goals



• work is peer reviewed and presented at national meetings, published

• co-mentors develop a long-term productive collaborative research relationship

Research Goals

Projects

Projects• represent facets of research programs in

biology


biology

• span range of biological scales


biology


• encompass a variety of areas from the mathematical sciences


biology



• cross-disciplinary pair of co-mentors, one from Biology, other from Math/CS/Stat


biology



• cross-disciplinary pair of co-mentors, one from Biology, other from Math/CS/Stat

• work started 1/1/2005, ongoing

Quantitative Identification of

Northeastern Missouri Bats via

Acoustic and Standard Surveys




• using Anabat bat detectors (zero-crossing analysis) to identify a bat to species





• creating a library of known calls (priors) for the nine species in Missouri





• creating a library of known calls (priors) for the nine species in Missouri

• taxonomic identification of bats; discriminant function analysis

The Effects of Prescribed Burning in

Grasslands on the Population

Structure of Predatory Beetles: a

Spatial Modeling Approach





•use spatial analysis as a tool in assessing the population structure of predatory ground beetles and field crickets in both burned and unburned grasslands






•discern if there is any significant preference among field crickets for burned or unburned habitat (mark recapture)






•discern if there is any significant preference among field crickets for burned or unburned habitat (mark recapture)

•pithfall traps, spatial statistics/analysis

The Aerodynamics of Saccate Pollen

and its Implications for Wind

Pollination



Pollination

•empirically and quantitatively verify the effects of pollen sacs in the wind dispersal of saccate pollen grains;



Pollination


•develop a mathematical model of pollen dispersal patterns and pollen settling speeds that can substitute for empirical testing.



Pollination



•electron microscopy; geometric/computer models



Pollination



•electron microscopy; geometric/computer models

Poster 13-8

GENEVA - Gene Expression

and Visualization Application



•computerized data extraction and visualization techniques applied to microarray data will reveal global gene expression patterns in the shoot apical meristem (SAM) tissues of maize




•students present results at Maize Meetings (Mexico, 2005)





•microarray data; MySQL and more

[CS team grafted to established research team]





•microarray data; MySQL and more

[CS team grafted to established research team]





•microarray data; MySQL and more[potential for long-term funded collaboration;

national Maize Project]

Mathematical Modeling of Plastron

Respiration in Dermacentor

variabilis (Acari: Ixodidae)




•determine if ticks respire under water via a plastron (first example of such in Ixodidae)





•predict underwater survivability of other species of ticks which show both interspecific and intergeneric morphological variation in spiracular plate structure





•predict underwater survivability of other species of ticks which show both interspecific and intergeneric morphological variation in spiracular plate structure

•use SEM to measure plastron structure and develop mathematical model of mechanism

Predicting occurrence of Missouri

Bladderpod (Lesquerella filiformis):

Modeling over space and time




•determine which habitat attributes most strongly influence the presence, absence and/or abundance of L. filiformis





•determine if the abundance of L. filiformis significantly change over time





•determine if the abundance of L. filiformis significantly change over time

•GIS environment; MANOVA, repeated-measures analysis, logistic regression (using SAS)

Image Analytic and Mathematical

Modeling of the Structure and

Dynamics of Biological Tissues




• image analytic computational utilities that are available as free software (measurements of in vitro vasculogenic structure and of the cell cycle in mouse epidermis)





• mathematical models of latter





• mathematical models of latter

Started Summer 2004; continued summer 2005Collaboration with KCOM

Programmatic Activities


• long-term research experiences


• long-term research experiences• summer:


• long-term research experiences• summer:-housed together in residence hall,


• long-term research experiences• summer:-housed together in residence hall,-meetings with team,


• long-term research experiences• summer:-housed together in residence hall,-meetings with team,-weekly workshops, and


• long-term research experiences• summer:-housed together in residence hall,-meetings with team,-weekly workshops, and-group meetings and discussions


• long-term research experiences• summer:-housed together in residence hall,-meetings with team,-weekly workshops, and-group meetings and discussions-meals together + (on Fridays) faculty mentors



• academic year: research (continues), monthly workshops, mathematical biology seminar



• academic year: research (continues), monthly workshops, mathematical biology seminar

• field trip to regional stakeholders (Donald Danforth Plant Science Center, Monsanto, etc.)

Discussions & Workshops


• Large group meetings (Mondays), mentor meetings (every third Monday)


• Large group meetings (Mondays), mentor meetings (every third Monday)-highs & lows, short term goals


• Large group meetings (Mondays), mentor meetings (every third Monday)-highs & lows, short term goals-informal questions/feedback


• Large group meetings (Mondays), mentor meetings (every third Monday)-highs & lows, short term goals-informal questions/feedback-gives sense summer community



• Discussions (Wednesdays), MathBio Workshop (Fridays)



• Discussions (Wednesdays), MathBio Workshop (Fridays)-topics related to professional, academic, and skill development




• Optional workshops




• Optional workshops (skills, mostly)

Discussions

•Preparing a research proposalDiscussions

•Preparing a research proposal

•Library training

Discussions


•Library training

•Reading the primary literature

Discussions


•Library training


•Keeping a research notebook or journal

Discussions


•Library training



•Giving an oral presentation

Discussions


•Library training




•Different modes of conducting research

Discussions


•Library training





•Ethics and responsible research conduct

Discussions


•Library training






•The importance of writing and submitting papers and grant proposals for peer review

Discussions


•Library training







•Conducting interdisciplinary research

Discussions


•Library training







•Conducting interdisciplinary research

•Data synthesis & presentation

Discussions

Workshops

•Using LateXWorkshops

•Using LateX

•Using Statistical Software

Workshops

•Using LateX


•Electron microscopy: A primer

Workshops

•Using LateX



•Image analysis & processing

Workshops

•Using LateX




•Conducting phylogenetic analyses

Workshops

•Using LateX





•Introduction to GIS for research applications

Workshops

•Using LateX






•Introduction to PERL & BioInformatics

Workshops

•Using LateX







•Using Excel

Workshops

•Using LateX







•Using Excel

•Using databases and database software

Workshops

•Using LateX







•Using Excel


•Editing digital images

Workshops

•Using LateX







•Using Excel



•Preparing posters for Truman's large format printer

Workshops

•Using LateX







•Using Excel



•Preparing posters for Truman's large format printer

•Finding and using open source software

Workshops

Community

Summer

Community

Summer

Community

Summer

Community

Summer

Community

Summer

Community

Summer

Community

Summer

Summer

Residence Hall

Small Group Meetings + MentorsWeekly Discussions/Workshops

Meals

Social EventsMathBio Seminar

Summer

Residence Hall

Small Group Meetings + MentorsWeekly Discussions/Workshops

Meals

Social EventsMathBio Seminar

Summer

• Image Analysis group (2004):- too many students- too many mentors- gave students too little direction, too

much lattitude

• curriculum reform (so far)

What’s Failed

• we’re thrilled with the way things are going

- student growth (intellectual, professional, skill sets)

- quality of science/mathematics- student ownership, enthusiasm- affect on faculty as researchers and

mentors

• we have a community of interdisciplinary scholars (students & faculty)

What’s Worked

• long-term nature has been critical to success

• when students live & eat together, they do talk shop with one another

• proposal presentation (summer week 3) was a trial by fire, but students raised the bar on one another!

• communication is difficult and critically important

Important Lessons

• the criteria for judging whether a course is interdisciplinary (cf. Newell) are different from those of research

• “This has completely changed the way I view my work.” (Dr. Laura Fielden)

• “[With the addition of the CS team] we’ve leaped an order of magnitude in what we are able to accomplish.” (Dr. Brent Buckner)

• “At the start, I wasn’t thrilled by the statistics, but now that we have data, I can’t wait to get to it.” (R. Rader)

• “I wish I could rewind my biology education and start it over in a way that had more mathematics.” (M. Mertz)

Thoughts

Acknowledgements• the students (11+)

• the colleagues (12+)

• Truman

• the MAA/AMS/CUR

• the National Science Foundation (DUE)

Acknowledgements• the students (11+)

• the colleagues (12+)

• Truman

• the MAA/AMS/CUR

• the National Science Foundation (DUE)

Thank you

Education

Truman's Mathematical Biology Program