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Motivation
Keeping track of the many emerging infections and epidemics is one of the most important endeavours in public health nowadays. Mathematical modelling comprehend a set of quantitative skills that pretend not only to help epidemiologist and public health officials and decision makers to better inform and address epidemics in real time, but also to learn from past epidemics in order to be more knowledgeable and better prepared for the next one.
Over the past years, the role of mathematical modelling in epidemiology has increased exponentially and with it the need to better understand, interpret and use the new body of knowledge from this research field. Also, this new approach represents and opportunity to integrate knowledge and skills from other fields such such mathematics, molecular biology, programming among others to better understand epidemics.
Within this course, the participants will be given an introduction to mathematical modelling from the theoretical and practical perspectives, using R software.
These are some of the questions that we will approach in this course:
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More information:
modelamiento@ins.gov.co
dide-bogotacourse@imperial.ac.uk
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Day 1: Monday June 17th, 2019 |
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Inauguración |
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Welcome |
PUJ |
Ministry of Health and Social Protection National Institute of Health (INS) |
08:00 |
Keynote talks Chair: Zulma Cucunubá |
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Martha Ospina |
INS |
The role of public institutions in the response to outbreaks and epidemics |
8:40 |
Anne Cori |
ICL |
Challenges for modelling epidemics and pandemics in real time: a conversation between academia and public institutions |
9:15 |
Coffee |
10:00 |
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Epidemics in Context Chair: Juan Vesga |
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Pierre Nouvellet |
ICL/Sussex |
RECON: A platform for collaborative and open source resources for data analytics and epidemics response |
10:20 |
Juliana Cuervo |
PUJ |
The role of Clinical Epidemiology in Outbreak and Epidemics Investigation |
10:50 |
Franklyn Prieto |
INS |
Epidemics in the context of an international migration crisis |
11:20 |
Natsuko Imai |
ICL |
How academia can inform global action for public health? An overview of outbreak analysis at MRC GIDA to support WHO |
11:50 |
Lunch |
12:20 |
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Experiences in Colombia Chair: Pan-American Health Organization |
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Marcela Mercado |
INS |
Laboratory and biologic induced research in the context of epidemics: the case of Zika and Chikungunya |
13:50 |
Marilyn Hidalgo |
PUJ |
Research in emerging infections: the case of Rickettsiosis in Colombia |
14:15 |
Zulma Cucunubá |
ICL |
Post-epidemic analyses. The promising use of modelling serological data to clarify the magnitude, dimension and impact of outbreaks. |
14:40 |
Juan Vesga |
ICL |
Understanding the recent trends of HIV notifications vs HIV incidence in Bogota |
15:05 |
Coffee |
15:30 |
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Panel and Discussion |
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Opportunities and challenges for the investigation and response to outbreaks and epidemics 16:00- 17:00 Chair: Marcela Mercado |
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Epidemics Simulation and coctel 17:00 - 19:00 |
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Day 2: Tuesday June 18th, 2019 |
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Talks AM: |
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Martín Rondón |
PUJ |
Introduction to Statistical Modelling |
8:10 - 9:00 |
Eddy Herrera Daza |
PUJ |
Statistics recap and data wrangling in R |
9:00 - 9:50 |
Coffee |
9:50 - 10:10 |
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Finlay Campbell |
ICL |
Reproducibility in R |
10:15 - 10:45 |
Anne Cori |
ICL |
Key data and questions for outbreak evaluation |
10:45 - 11:45 |
Javier Díaz |
INS |
Data workflow during epidemics in Colombia |
11:45 - 12:30 |
Lunch |
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Practical PM Coordinators: Zulma Cucunubá, Kelly Charniga & Finlay Campbell Support: all Participants will have a hands-on practical to intermediate use of R as a statistical programme with emphasis in reproducibility, data management and transparency in data and methods. R packages: Tidyverse, Ggplot2, Incidence, Discrete, EpiTricks |
14:00 - 17:00 |
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Day 3: Wednesday June 19th, 2019 |
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Talks AM: |
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Pierre Nouvellet |
ICL |
Introduction to modelling of infectious diseases |
8:30 - 9:30 |
Anne Cori |
ICL |
R0, Rt and their estimation methods during epidemics (EpiEstim Package) |
9:30 - 10:30 |
Coffee |
10:30 - 10:50 |
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Pierre Nouvellet |
ICL/Sussex |
Methods for Short Term Projections in epidemics (Projections Package) |
11:00 - 11:45 |
Finlay Campbell |
ICL |
Framework for integrating epidemiological and genetic data to reconstruct outbreaks (Outbreaker2 Package) |
11:45 - 12:30 |
Lunch |
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Practical PM Coordinators: Anne Cori & Natsuko Imai Support: all It includes content on the estimation of key delays (e.g. incubation period, serial interval) and the characterisation of the underlying distributions, the estimation of growth rates, doubling times, of the basic reproduction number, case fatality ratio and simple short-term forecasting. R packages: EpiEstim, Projections, Outbreaker2 |
13:30 - 17:00 |
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Day 4: Thursday June 20th, 2019 |
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Talks AM: |
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Daniela Olivera |
ICL |
Introduction to Dynamic models for VBD |
8:30 - 9:30 |
Kelly Charniga |
ICL |
Gravity models for arboviruses |
9:30 - 10:30 |
Coffee |
10:30 - 10:50 |
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Zulma Cucunubá |
ICL |
Force-of-Infection Models for vector borne disease |
10:30 - 11:45 |
Arran Hamlet |
ICL |
Modelling Yellow Fever in Latin America |
11:15 - 12:00 |
Lunch |
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Practical PM Coordinators: Zulma Cucunubá, Arran Hamlet & Daniela Oliveira Support: all The aim is to gain a general understanding on the role of modelling on the main vector borne diseases, with special emphasis on Malaria, Chagas and Zika. R packages: Odin, Desolve |
13:30 - 17:00 |
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Day 5: Friday June 21st, 2019 |
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Talks AM: |
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Martha Murcia |
UNAL |
Molecular microbiology of TB in Colombia/ M. colombiense. (TBC) |
8:00 - 8:30 |
Juan F. Vesga |
ICL |
Modelling and evaluation of interventions to control TB in different epidemic contexts |
9:30 - 10:30 |
Coffee |
10:30 - 10:50 |
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Zulma Cucunubá |
ICL |
Modelling measles outbreak in Latin America |
11:00 - 11:30 |
Igor Siveroni |
ICL |
Outbreak Phylogenetic Analysis using Genetic Data |
11:30 - 12:00 |
Juan F. Vesga |
ICL |
TB/HIV transmission dynamics applied to mathematical modelling |
12:00 - 12:30 |
Lunch |
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Practical PM Coordinators: Juan Vesga & Igor Siveroni Support: all The aim is to gain a general understanding on the role of modelling on modelling and informing control of two global epidemics such as HIV and TB. |
13:30 - 15:30 |
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Final Remarks |
16:30 - 17:00 |
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International Speakers and Instructors
Dr Anne Cori Imperial College London |
Dr. Anne Cori is an applied mathematician by training, she has been doing research on infectious diseases for over 10 years on a range of pathogens, including influenza, SARS, Ebola, MERS, and HIV. She has been heavily involved in real-time analysis of outbreak, particularly the West African (2015) and the DRC(2018) epidemics, as well as the MERS epidemic in Saudi Arabia and the yellow fever outbreaks in Angola/DRC and in Brazil. She has developed a range of generic methods and R packages to address recurring public health questions during outbreaks. She is the methodology coordinator for the R Epidemics CONsortium (RECON). |
Dr. Pierre Nouvellet Honorary Reader, |
Dr Pierre Novellete’s current research focuses on developing statistical methods to estimate relevant parameters within complex ecological settings. He integrates various sources of information in order to better understand the dynamics of diseases’ transmission and mitigate their public health risk. The focus of his current work concentrates on 3 themes: 1.) Vector-borne and zoonotic diseases, with a strong focus on rabies and Chagas disease. 2.) Emerging diseases, with a strong focus on MERS-CoV, Ebola, Zika and antibiotic resistance. 3.) Rapid response to outbreaks and real-time analysis, with a strong focus on developing tools and capacity ahead of future outbreaks. |
Dr Zulma Cucunubá MD, PhD MRC GIDA Imperial College London |
Dr Zulma Cucunubá is currently a MRC Research Fellow in the Department of Infectious Disease Epidemiology at Imperial College London. Her research focuses on the use of statistic and mathematical methods to evaluate the magnitude of infectious disease spread and impact of interventions. Previously she worked as postdoctoral researcher for the Vaccine Impact Modelling Consortium (VIMC). Her trajectory includes the developed of a substantial body of research on Chagas Disease in Latin America including various multilateral projects. More recently she has expanded her research interests to other emerging infections such as Zika, Chikungunya, and epidemics response in Latin America. |
Dr Juan F Vesga Research Associate Imperial College London |
My research at the Department of Infectious Disease Epidemiology focuses on applying mathematical and statistical methods to assess the dynamics of infectious disease and the impact of interventions. The main focus of my research being on Tuberculosis and HIV. |
Dr Natsuko Imai WHO Liaison MRC GIDA Imperial College London |
Dr Natsuko Imai is the liaison between the MRC Centre for Global Infectious Disease Analysis and the World Health Organization. She is responsible for developing and co-ordinating projects to support WHO activities and departments including The Global Influenza Programme, The Initiative for Vaccine Research, and the Global Outbreak Alert and Response Network. As a whole, the Centre provides technical assistance in several disease areas including malaria, HIV, yellow fever, influenza, polio, hepatitis, and dengue. |
Finlay Campbell PhD Student MRC-GIDA Imperial College London. |
Finlay Campbell is a PhD student in the Department of Infectious Disease Epidemiology at Imperial College London. His research focuses on the development of statistical and computational tools for estimating transmission chains combining epidemiological and genetic data. This approach seeks to improve outbreak response in real-time by providing actionable epidemiological insights from data collected in the field. Finlay is an active member of the R Epidemic Consortium (RECON), maintaining and contributing to multiple packages (outbreaker2, outbreaks, epicontacts) as well as running capacity-building workshops. Finlay have also assisted the WHO in responding to the 2018/2019 Ebola response in DRC and was seconded to Geneva for one month to analyse the incoming data in-house. |
Dr. Igor Siveroni Scientific Software Developer. MRC-GIDA. |
Dr. Igor Siveroni is a Computer Scientist working as a Scientific Software Developer at MRC-GIDA. His current work focuses on the implementation of software for mathematical modelling of infectious diseases and the analysis and intepretation of pathogen genetic sequence data. He is the main developer of PhyDyn, a BEAST2 package for performing Bayesian phylogenetic inference under models that deal with structured populations and complex population dynamics. |
Kelly Charniga PhD Student MRC-GIDA |
Kelly is a PhD student at the MRC Centre for Global Infectious Disease Analysis of the Department of Infectious Disease Epidemiology at Imperial College London, UK. With a background in biology and epidemiology, she is currently studying the spatial and temporal dynamics of Zika and chikungunya viruses in Colombia. She has done internships at the Detroit Health Department and the U.S. Department of Homeland Security and has volunteered in bat conservation efforts. Her research interests include emerging infectious diseases, zoonoses, and biosecurity. https://www.imperial.ac.uk/people/k.charniga17/research.html |
Daniela Olivera PhD Student MRC-GIDA |
Daniela is a PhD student at the MRC Centre for Global Infectious Disease Analysis of the Department of Infectious Disease Epidemiology at Imperial College London, UK. Currently, she is studying disease eradication models coupled with health economics theory for optimal resource allocation. Before her doctoral studies, Daniela studied the dynamics of different vector borne disease models at Universidad de los Andes in Bogotá. |
Arran Hamlet |
Arran is a PhD student in the department of Infectious Disease Epidemiology at Imperial College London. His primary research focuses on the epidemiology of yellow fever (YF) in South America, the role of non-human primates in transmission and the potential for expansion of the endemic zone. Arran’s previous work has involved coordinating with the World Health Organization (WHO) to provide real-time outbreak analysis, and to inform the targeting of vaccination campaigns in response to YF outbreaks in Angola, the Democratic Republic of the Congo and Nigeria. |
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National Speakers and Instructors
Martha Lucía Ospina Martínez. Directora General INS |
Martha Lucia Ospina is a Physician from the Universidad Javeriana, a master’s degree in Epidemiology from the Universidad del Valle and in Health Economics from the Pompeu Fabra University of Spain and a specialist in Public Health Management from the ICESI university. Linked to the health sector for 25 years, where she has occupied, among other positions, the Director of the High Cost Account of Colombia. Director of Epidemiology and Demography of the Ministry of Health and Deputy Minister of Health in charge. He led the formulation of the Ten-Year Public Health Plan for Colombia, the construction of the ASIS (Health Situation Analysis), at the national level, the reordering of the national population studies and surveys agenda and the Comprehensive Social Protection Information System (SISPRO). He has held the Chair of Risk Management in Health at the Javeriana University for 10 years. She is currently the Director of the National Institute of Health, being the first woman in 100 years to hold this position. |
Franklyn Edwin Prieto Director Vigilancia INS |
Franklyn Prieto is a Physician, Doctor of Public Health, Master of Public Health and Bioethics, specialist in Epidemiology and field epidemiologist of the program of the National Institute of Health. He has developed projects for the prevention and control of HIV and reduction of HIV mother-to-child transmission carried out by the National Institute of Health, UNAIDS and Federesalud. In addition, she was a Health Specialist in the Global Fund project “Young people in situations of displacement and their vulnerability to HIV”, in 48 municipalities in the country. He has been a manager of hospital HIV programs, Hospital Extension and comprehensive IPS. He has been a consultant for the Centers for Disease Control and the Pan American Health Organization and is currently the director of Public Health Surveillance at the National Institute of Health |
Marcela Mercado Reyes Coordinadora Grupo de investigación en Salud Materna y perinatal INS |
Marcela Mercado is Bacteriologist and Magister in Clinical Epidemiology at the Javeriana University. She has been a university professor of epidemiology and biostatistics. She is currently Coordinator of the research group on Maternal and Perinatal Health at the National Institute of Health. She has been a researcher in projects related to vector-borne diseases, evaluation of health technologies, analysis of diagnostic tests and effectiveness of vaccines among others. She is currently the principal investigator of two Zika projects in pregnant women infected during the epidemic 2015 - 2016. These projects have contributed to the generation of knowledge about the natural history of the disease, its complications and the role of the confection of Zika and with other arboviruses transmitted by aedes aegypti |
Jorge Díaz Coordinador del Centro de Operaciones de Emergencias INS |
Physician, epidemiology specialist, coordinator of the Risk Management, Immediate Response and Risk Communication Group and the Emergency Operations Center in Public Health of the National Institute of Health. He has been a leader in the response to epidemiological surveillance in public health emergency situations of transmissible events, natural disasters and emergent and reemerging events. Link: jdiaz@ins.gov.co |
Dra Martha Murcia Profesora Titular Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia. |
Dr Martha Murcia is currently professor at the Department of Microbiology, Faculty of Medicine, The National University of Colombia. Her field of research focuses on infections caused by mycobacteria, especially Mycobacterium tuberculosis and Mycobacterium avium complex (MAC). She has led several projects that have allowed the diagnosis of active and latent tuberculosis, as well as mycobacteriosis in HIV-infected individuals: inmates population and in indigenous population. In addition she has worked in molecular epidemiology of tuberculosis projects, as well as resistance of M. tuberculosis. |
Marilyn Hidalgo Ph.D |
I am a Bacteriologist with Master’s Degree in biology focused on the study of microorganisms of public health importance. I obtained my Ph.D. in biological sciences at Andes University in Colombia. As part of my doctoral dissertation I studied Rickettsias as etiological agents of febrile illness in Colombia, and some of my training in that particular area was conducted at the University of Texas Medical Branch. After obtaining my Ph.D. degree I began to study the ecology of arthropod-borne diseases in endemic areas of Colombia. Within my research as leading researcher I focused mainly on the following two aspects: 1. Assessing the current state of murine typhus in a specific department of Colombia 2. Studying the ecology of ticks as vectors of Rickettsia. Importantly, my approach is based on interdisciplinary studies, including biologists, microbiologists, engineers, ecologists, epidemiologists. |
Martín Rondón Profesor Asociado |
Martín is a statistician from the Universidad Nacional de Colombia with a Master’s degree in Biostatistics from Universidad de Chile. He is Associate Professor in the Department of Clinical Epidemiology and Biostatistics at Universidad Javeriana, where he conducts teaching and research. He also participates in different research projects as a consultant or statistical consultant |
Juliana Cuervo MD. PhD. Assistant Professor School of Medicine at Javeriana University |
Dr. Juliana Cuervo is an assistant professor in the department of clinical epidemiology and biostatistics in the School of Medicine at Javeriana University in Bogotá. She holds a medical degree, a master’s degree in Clinical Epidemiology from Javeriana University, and a PhD degree in Epidemiology from the Johns Hopkins University Bloomberg School of Public Health in the United States. Her work has focused mainly on HIV, Tuberculosis, and cardiovascular disease in the context of HIV infection. Dr. Cuervo has worked in Colombia, Papua New Guinea, Ethiopia, Kenya, Namibia, Botswana, Malawi, Tanzania, Zambia, Cameroon and Rwanda. |
Eddy Herrera PhD Student Profesor e investigador Matematicas Estadistica Universidad Javeriana |
Eddy is a PhD candidate in Engineering. Specialist in Management, programming, construction of tools (web applications) and packages in R. She works on projects where Mathematical modeling, Statistics and Stochastic programming support research in the areas of Science and Engineering |
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