Pasteur course MODELING OF INFECTIOUS DISEASES
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1 Pasteur course MODELING OF INFECTIOUS DISEASES PROGRAM
2 Modeling of Infectious Diseases CO-DIRECTORS OF THE COURSE Pierre -Yves BOËLLE Université Pierre et Marie Curie Hôpital Saint Antoine INSERM UMR S ,ure de Chaligny Paris Tel +33(0) boelle@u707.jussieu.fr Unité de Recherche et d Expertise Epidémiologie des Maladies Emergentes Institut Pasteur 25,28 rue du Dr Roux Paris Cedex 15 Tel +33(0) romulus.breban@pasteur.fr Director of the Epidemiology and Public Health department Joint director of the Pasteur-Cnam School of Public Health Arnaud FONTANET Emerging Disease Epidemiology Unit Institut Pasteur - Paris, France
3 COURSE PRESENTATION This course is intended to provide students in sciences, medicine and public health with a thorough introduction to the mathematical modeling of infectious diseases. A college degree is required. Basic knowledge of matrix algebra, calculus and probability is highly recommended. The class makes a basic exposition of the fundamental concepts used in the mathematical modeling of infectious diseases and their relation to empirical data. Particular attention is devoted to developing compartmental models describing the spread and control of various infectious diseases with respiratory, sexual or vector-borne transmission. Then, mathematical realizations and corresponding computer implementations of compartmental models are presented within either a deterministic or stochastic framework. The class also covers modeling of disease transmission networks using homogeneous branching processes and its applications to describing disease invasion. More sophisticated models of transmission networks embedded within complex networks of social contacts and/or travel networks are discussed, as well. Uncertainty and sensitivity analyses of modeling output are explained and illustrated using the software R, Excel and SaSAT. The notion of the basic reproduction ratio R0 is introduced for models of various types and its epidemiological role thoroughly explained. Methods to calculate R0 from epidemiological data and the impact of control measures on R0 are discussed. Lectures alternate with computer exercises using the R, Excel and SaSAT software, and modeling case studies from the scientific literature. A journal club meeting is scheduled toward the end of the class when scientific papers are discussed in the light of the presented material.
4 FIRST WEEK - April 16 20, 2018 MONDAY, APRIL, 16 9:00-9:30 Welcome of the students Registar office Introduction to the course Pierre-Yves BOELLE 9:30-12:30 Using mathematics to gain biological insight Troy DAY (Queen s iversity, Canada) 14:00-17:00 The SIR model: formulation, analysis, Lulla OPATOWSKI discussion + R exercise (Institut Pasteur, Paris & UVSQ) TUESDAY, APRIL, 17 9:00-12:30 From disease description to compartmental model formulation 14:00-17:00 Model and simulation: deterministic versus stochastic + R exercise WEDNESDAY, APRIL 18 9:00-12:30 Likelihood: from data to parameters Pierre-Yves BOELLE + R exercise 14:00-17:00 Back-calculation: article case study Virginie SUPERVIE (INSERM & Univ. Paris VI) THURSDAY, APRIL, 19 9:00-12:30 Disease invasion: birth & death processes + R exercise 14:00-17:00 Disease transmission: homogeneous branching processes + article case study FRIDAY, APRIL, 20 9:00-12:30 Analysis of transmission chains: the case of SARS Pierre-Yves BOELLE + R exercise Choice of paper for discussion 14:00-17:00 Article reading (personal work)
5 SECOND WEEK - April 23 27, 2018 MONDAY, APRIL 23 9:00-12:30 Building SIR models in R Pierre-Yves BOELLE 14:00-17:00 R0 calculation: a general recipe TUESDAY, APRIL 24 9:00-17:00 Estimating R0 from data: practical methods Pierre-Yves BOELLE + R exercise WEDNESDAY, APRIL 25 9:00-12:30 Predicting the effect of interventions with the reproduction number 14:00-17:00 The saga of interventions: modelling public participation to vaccination programs THURSDAY, APRIL 26 9:00-12:30 Vector borne disease modelling Timothée VERGNE + R exercise (UMR ENVT-INRA 1225, Toulouse) 14:00-17:00 Workshop: article discussion Pierre-Yves BOELLE FRIDAY, APRIL 27 9:00-12:30 Mixing: from random to realistic networks Chiara PO LETTO (INSERM & Univ. Paris VI) 14:00-16:00 Examination Pierre-Yves BOELLE Examination: The class ends with a written, individual-level evaluation scheduled to last two hours. To answer the exam questions, students have at their disposal all the materials and software used in class
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