<p> FEScUE summer 2010</p><p>April/May  Matrix models (Sarah)  Sensitivity for matrix models (Sarah)  Last year's project on killer whales developed by Don and Megan </p><p>June Mathematical Theme: Sensitivity analysis for nonlinear odes and maps Biological Theme: Disease Ecology and Genetics Software Tools: Matlab, Maple, LATeX Writing for publication: Super-cluster #1 (See FEScUE Summer 2010 SENSAI Project.pdf) First and second year FEScUE students will form pairs comprising one mathematics student and one life sciences student (one 1st year student and one 2nd year student). Each pair will investigate one of six different models for the interaction of genetics and disease in Tribolium. Specifically, each pair will consider either partial dominance, over dominance or frequency dependence, and selection pressure via either viability or fecundity. Each pair will consider multiple models for disease transmission, e.g., frequency dependence vs. density dependence. Solution of the models and their sensitivity analysis will be conducted using SENSAI. A section for a common manuscript will be prepared using LATeX. Cluster #2 Second year student Mike Mikucki and others (TBA) will complete genetics analyses for SENSAI paper and prepare results for publication. Deliverables: o Sections for Tribolium genetics of resistance paper o SENSAI paper o Refinement of SENSAI as a teaching tool for population genetics, disease and evolution</p><p>July During July the cohorts split in to one of a number of possible projects in disease ecology and a study group in structural biology.</p><p>Disease Ecology a) Small world models and their sensitivity analysis (Antolin/Tavener)</p><p>1  Small world models using stochastic models (rather than continuous models on networks which currently model geographic isolation but not small populations)  Sensitivity analysis for stochastic processes (small copy numbers)  Deliverable: who knows, but a new approach to small world modeling b) Genetics models with stochastic parameters (Antolin/Tavener)  Sensitivity analysis using stochastic collocation and sparse grid techniques  Deliverable: SENSAI_v2 c) Chronic Wasting Disease  disease + genetics + gender model building (Antolin/Hobbs/Tavener)  field work and data analysis (Boone/Hoeting)  laboratory work (Antolin/Galloway)</p><p>Structural Biology  study group [Hansen/Shipman/Tavener] (reading and preparation for summer 2012)</p><p>Potential future study groups (2011)  Nial Hanan and Gerhard Dangelmayr (Savanah)  James Liu and Chaoping Chen (ultra-centrifugation / reaction-diffusion-convection processes in cells)  Jay Breidt, Don Estep, Jennifer Mueller and Karolin Luger (SAXS)</p><p>2 Weekly schedule 1. Monday 1. 8:30am—10:00 am WB223A: Weekly organizational meting 2. 10:00am—12:00 am Professional development / speakers 3. 1:30pm—4:30pm Independent study 2. Tuesday 1. 9:00am—12:00pm Independent study / Reading group 2. 1:30pm—4:30pm WB223A 3. Wednesday 1. 8:30am—10:00am Presentations by Mike, Simon, Sarah or Stu 2. 10:00—12:00 WB223A 3. 1:30pm—4:30pm Independent study 4. Thursday 1. 9:00am—12:00pm Independent study / Reading group 2. 1:30pm—4:30pm WB223A 5. Friday 1. 8:30am—10:00 am Summer reading presentations 2. 10:00 am —12:00 am WB223A 3. 1:30pm—4:30pm Independent study</p><p>Field trips -- TBA</p><p>3 Summer Reading list First Year reading  Heppel, S.S. 1998. Application of life-history theory and population model analysis to turtle conservation. Copeia, 1998: 367-375.  Hughes, T.P. 1984. Population-dynamics based on individual size rather than age - a general-model with a reef coral example. Am. Nat. 123: 778-795,  Oli, M. K., M. Venkataraman., P. A. Klein, L. D. Wendland, and M. B. Brown. 2006. Population dynamics of infectious diseases: A discrete time model. Ecological Modelling 198:183-194.  Platt, J.R. 1964. Strong inference. Science 146: 347-353  Cohen, J.E. 1976. Irreproducible results and the breeding of pigs (or nondegenerate limit random variables in biology). Bio Science 26, 391-394.</p><p>Second Year reading Population, genetics and evolution of disease resistance TBA</p><p>First & second year reading  D.M. Hamby: "A review of techniques for parameter sensitivity analysis of environmental models" (Simon)  Caswell H. 2008. Perturbation analysis of nonlinear matrix population models. Demographic Research. 18: 59-116.  Blaser M, Paul Schmid-Hempel P. 2005. Determinants of virulence for the parasite Nosema whitei in its host Tribolium castaneum. Journal of Invertebrate Pathology. 89: 251-257.  More Tribolium papers</p><p>Liberal Arts reading (first & second year) . "The Music of Life: Biology Beyond Genes", by Denis Noble . "Rosalind Franklin: The dark lady of DNA", by Brenda Maddox . "Collapse: How societies choose to fail or survive", by Jared Diamond . "Renewable energy -- Without the hot air", by David Mackay</p><p>Reading for CWD: Distribute Williams (2005), Miller et al. (2006), Distribute Fox et al. (2006), Jewell et al. (2007)</p><p>4 Week-by-week schedule</p><p>Sensitivity analysis in disease ecology and genetics</p><p>Week 1 June 1- June 4: </p><p> o Monday: Federal Holiday o Tuesday: Introduction and planning o Wednesday: SENSAI (Simon) o Thursday: LATeX (Simon or Sarah) o Friday: SENSAI (Simon)</p><p>Week 2 June 7 - June 11</p><p> o Monday: LATeX (Simon or Sarah) o Tuesday: SENSAI (Simon) o Wednesday: Oli et al - 2nd years lead discussion o Thursday: D.M. Hamby, "A review of techniques for parameter sensitivity analysis of environmental models", (Simon) o Friday: Book review "The music of life", Dennis Noble</p><p>Week 3 June 14 - June 18</p><p> o Monday: Evolution paper + Population genetics (Mike Antolin) o Tuesday: Tribolium (Mike Antolin) o Wednesday: Tribolium (Mike Antolin) o Thursday: Work in pairs (computing) o Friday: Work in pairs (computing)</p><p>Week 4 June 21 - June 25</p><p> o Monday: Work in pairs (computing) Professional development: hypothesis testing (First years read “Strong Inference”, Second years optional) o Tuesday: Work in pairs (computing) o Wednesday: Work in pairs (writing) o Thursday: Work in pairs (writing) o Friday: Work in pairs (writing) Book review: “Dark Lady of DNA”.</p><p>5 CWD, small world problems, sensitivity for stochastic models, structural biology reading group </p><p>Week 5 June 28 - July 2</p><p>Week 6 July 5 - July 9</p><p> o Friday: Book review</p><p>Week 7 July 12 - July 16</p><p>Week 8 July 19 - July 23</p><p> o Friday: Book review</p><p>Week 9 July 26 - July 30</p><p>Students</p><p>Cohort #3 Drew Neavin Biological Sciences [email protected] Sophmore Elizabeth Moses Biological Sciences [email protected] Junior Kyle Strand Mathematics [email protected] Junior Lauren Chase Mathematics [email protected] Senior Lauren Gillott Mathematics [email protected] Senior Leslie Wooten Biological Sciences [email protected] Freshman </p><p>Cohort #2 Ethan Costain Biological Sciences [email protected] Junior Radia Dakhama Biological Sciences [email protected] Junior Jesse Drendel Mathematics [email protected] Junior Moriah Echlin Biological Sciinces [email protected] Senior David Hopkins Mathematics [email protected] Senior+ Michael Mikucki Mathematics [email protected] Senior+ Samantha Parks Biological Sciences [email protected] Junior Reid Thornton Mathematics [email protected] Senior+</p><p>6</p>