Sponsored by the Department of Biology, Colorado State University, with funding provided by the National Science Foundation


When: June 1-4, 2008
Who: Graduate students and post-doctoral researchers

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.

Instructors:  Mike Antolin, Ben Bolker, Ottar Bjornstad, Andy Dobson, Colleen Webb, Roman Biek, Aaron King, Cecile Viboud



Venue:   Yates Hall (see campus map)


Day 1:  Group instruction in basics of data manipulation in Excel, R, and basic population genetics software.

Days 2-3: 
            8 – 12:             Instruction via lectures and computer exercise/demonstrations   
            12 – 1pm:        Lunch (provided)
            1pm – 5pm:     Work in groups on data analyses and modeling

Day 4:
            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)


Registration for credit:  CSU Continuing Education (students will be notified of acceptance to workshops with instructions for registration)

Financial aid: With application and acceptance into the workshop, financial assistance for graduate students and postdocs covering the $500 workshop tuition fee and up to $500 reimbursement for travel and housing will be available.