Ecology and Evolution of Infectious Diseases

Workshops on Modeling and Data Analysis

Sponsored by the Department of Biology, Colorado State University

With funding provided by the National Science Foundation

Dates: May 17-20, 2009
Who: Graduate students and post-doctoral researchers

NOTE TO ALL WORKSHOP PARTICIPANTS: The workshops begin at 8:30 am on Sunday May 17. Please report to room 350 (third floor) of the Miller Student Learning Center for the introduction and orientation. Click on the links below for directions and a map to the location.

Venue: Zell B. Miller Student Learning Center, Rooms 368-372

UGA Campus (click here for a campus map)

The Holiday Inn and Express are at the top left corner of the campus map on Broad Street, and the Miller Learning Center is located just northwest of Sanford Stadium.


Ecology Workshop Instructors: Ben Bolker (University of Florida), Aaron King (University of Michigan), John Drake (University of Georgia), Matt Ferrari (Penn State University)

Evolution Workshop Instructors: Colleen Webb (Colorado State University), Roman Biek (University of Glasgow), Mike Antolin (Colorado State University)


Ecology of infectious disease curriculum.The content of this workshop emphasizes mathematical models of disease ecology, basic and advanced statistics skills, and sessions on how to query long-term data sets for estimating parameters, exploring temporal fluctuations and investigating spatial patterns. Specific goals include:

1) To provide participants with skills for exploring long-term data trends and estimate population parameters (R0, β) that would fit infectious disease models.
2) To develop frameworks for observations or experiments needed to test hypotheses and analyze longitudinal and vertical data sets on disease incidence and parasite intensity.

A key to success of the workshop is assess the interests and abilities of participant before the workshop and organize complementary groups of 4-5 participants that include individuals with complementary data and skills.  This will be accomplished by a questionnaire sent to registrants several weeks before the workshop, then organizing them into groups of five, matched by 1.) types of data they have, 2.) skills the students possess (programming in C++, Matlab, S-plus and R), 3.) general areas of interest expressed by the students (organisms:  e.g. vertebrate (including humans) or invertebrate animals, plants; areas of analysis: e.g. time series, ODE modeling and stochastic realizations, spatial models).  In addition, we will provide standards for data files (computer-ready form: comma or tab delimited flat file in ASCII, Excel preferable).

Evolutionary biology of infectious diseases curriculum. This workshop will provide students with an understanding of relevant concepts in addition to practical phylogenetic and population genetic tools they can apply in their own research. The workshop will be particularly suitable for infectious disease ecologists interested in pathogen evolution and emergence, and for researchers in public health and the biomedical fields interested in how pathogens evolve both within hosts/patients (e.g. HIV), host immunogenetics, and how interventions (antimicrobial drugs, vaccinations) affect the evolution of pathogens.  Specific goals include:

1.) To familiarize participants with analysis of host and pathogen genetics and phylogenetics, and relate these to identifying reservoir populations, detecting natural selection, and evaluating recombination and reassortment in pathogens.
2.) To provide practical training in experimental design and hypothesis testing frameworks that can be applied to the participants’ genetic data, or to data sets collected from databases like GENBANK.

Again, a key to success will be to determine students’ interests and abilities before the workshop.  A questionnaire sent to registrants several weeks before the workshop will aid in organizing complementary groups of 4-5 participants, matched by 1.) types of data to share, 2.) skills (knowledge of genetics, familiarity with phylogenetic and population genetic software, and 3.) general areas of interest (organisms: e.g. viruses, bacteria, or fungi; areas of analysis: e.g. relationships between emerging pathogens and wild reservoirs, host-specific selection).  We will provide format standards for data.

Tentative Agenda

May 17:  Group instruction in basics of data exploration in Excel, R, and basic population genetics software.

May 18-19: 
            8 – 12:             Instruction via lectures and computer exercise/demonstrations   
            12 – 1pm:        Lunch (provided)
            1pm – 5pm:     Work in groups on data analyses and modeling

May 20 :
            8 – 12:             Work in groups on data analyses and modeling
            12 – 1pm:        Lunch (provided)
            1pm – 5pm:     Groups report results to entire audience (both ecology and evolution together)