Announcements June 15, 2016

E²M²: Ecological and Epidemiological Modeling in Madagascar


Announcing the Inaugural Clinic –

E²M²:  Ecological and Epidemiological Modeling in Madagascar

November 27-December 3, 2016

Centre ValBio, Ranomafana National Park, Madagascar


CLICK HERE to download the application!

Deadline EXTENDED: September 1, 2016

We are pleased to announce the inaugural E²M²:  Ecological and Epidemiological Modeling in Madagascar clinic, to be held November 27-December 3, 2016 at Centre ValBio, Ranomafana National Park, Madagascar. The clinic will be a one-week intensive workshop aimed to provide an introduction to the use of dynamical models in understanding ecological and epidemiological data.

Students will participate in a series of interactive lectures and computer-based tutorials and learn to fine-tune model-based research questions, develop clear model frameworks and corresponding equations, and fit models to real-world data. All students will work closely with peers and faculty to develop a research plan for an ongoing or existing project integrating dynamical modeling with data collection and/or analysis in a biological system of their choosing. These research plans can then be used as a foundation for future dissertation or grant proposals.

The course will be targeted towards students in their third cycle or higher in biology, mathematics, medicine, public health, or related fields, though all are welcome to apply. The course will be taught primarily in English, though a subset of the faculty will be available to offer some translation into French and/or Malagasy. A working knowledge of the English language is required for admission; however, we will do our best to make the material accessible to students who find English challenging. If you have any questions about the appropriateness of your background or training for our course, either in language or in science, please do not hesitate to contact us straight away (email below).

Funding is available to cover transportation from Antananarivo to Ranomafana and back, in addition to room and board throughout the duration of the clinic for all participants. The application process is expected to be highly competitive.

Applications are available at and will be due on September 1, 2016 via email to Cara Brook ( Please do not hesitate to email Cara or Tanjona Ramiadantsoa ( with any questions or concerns. We hope to see you in November!

Thank you, and best,

The E²M² instructor team

Matthew Bonds, Cara Brook, Andres Garchitorena, Jessica Metcalf, Calistus Ngonghala, Juliet Pulliam, Tanjona Ramiadantsoa, Hafaliana Christian Ranaivoson, & Amy WesolowskiPreliminary Syllabus

Preliminary Syllabus

Sun, Nov 27:
Depart from Tana via bus, travel to Ranomafana (lunch stop Antsirabe)
On bus: Icebreakers
Introduction and Road map: What are we doing here?
Lecture: What is Science? Exploring Models and Data
Real-world examples of models applied to data in Madagascar (and other) systems
Case study: Persistence of plague in the Malagasy highlands

Mon, Nov 28:
Early Morning:
Lecture: Simplification for Generalization: Intuitive Aspects of Dynamics and Introduction to Model Worlds
From early predator-prey dynamics to host-parasite interactions
Late Morning:
Exercise: Dynamical Fever
Lecture: The SIR Model Family: Conceptual Framework and Introduction to Differential Equations
R-tutorial: Introduction to Model Implementation in Discrete and Continuous Time
Late Afternoon:
Group Journal Club: Discussion of scientific article
Writing Exercise: Formulating research questions (HW for tomorrow)
Faculty Research Presentations

Tues, Nov 29:
Early Morning:
Lecture: Variability in Models: Incorporating Heterogeneity
R-tutorial: Heterogeneity in SIR models
Late Morning:
Small group session: Refining research questions for modeling projects
Early Afternoon:
Lecture: Modeling in Practice: The Life Cycle of a Modeling Project, from Conception to Publication
Writing Exercise: Creating a model world to address a research question (HW for tomorrow)
Mentored working session
Late Afternoon:
Mid-Session Feedback
Night hike in Ranomafana National Park with rodent trapping for infectious disease data collection

Wed, Nov 30:
Early Morning:
Quick agenda item: Recap mid-session feedback
Lecture: Stochastic Simulation Models
R-tutorial: Stochastic Simulation Models
Late Morning:
Small Group Session: Model Telephone
Early Afternoon:
Lecture: Metapopulation Models, Extinction, and Persistence
R-Tutorial: Plague Persistence in Madagascar
Late Afternoon:
Lecture: Model Fitting by Many Methods: Minimizing Squared Differences, Likelihood, and Bayesian Methods
Evening: Faculty research presentations

Thurs, Dec 1:
Early Morning:
R-tutorial: Model Fitting in Practice, using our own field data from Tuesday night
Late Morning:
Mentored working session: Refining model worlds
Early Afternoon:
Group hike in Ranomafana National Park
Late Afternoon – Evening:
Mentored working session: Finalize research plans for tomorrow

Fri, Dec 2:
Early Morning:
Lecture: Local and Global Uncertainty and Sensitivity Analyses
R tutorial: Exploring Uncertainty
Late Morning:
Lecture: Model Evaluation and Comparison
Presentation of research proposals
Farewell party

Sat, Dec 3:
Early morning:
Final feedback session
Return to Antananarivo via bus


CLICK HERE to download the application!

Application deadline: September 1, 2016