Summer School and Workshop on Modeling and Numerics in Epidemiology

As first event of SaC³ we organize a one week summer school and conference at the Universidad del Valle in Cali, Colombia. This webpage is under construction (Sep 25, 2024). Information, in particular on the registration process, will follow soon.

Date and location

Universidad del Valle, Cali, Colombia
December 9-13, 2024

Venue

The school will be held in the Michel Valero auditorium of the Departamento de Física located on the second floor of the E20 building (Facultad de Ciencias Naturales y Exactas), and the workshop in the Jürgen Tischer computer center of the Departamento de Matemáticas, located on the third floor of the same building. The E20 building is located on the Campus Melendez (campus map) of the Universidad del Valle in Cali, Colombia.

Examples for very good hotels in the are are Hotel NH Cali Royal or Hilton Garden Inn Cali Ciudad Jardin. The area is in general safe and we recommend that you look for accomodation close by.

Contents

The Summer School consists of a series of lectures on different topics in mathematical epidemiology, covering aspects of modeling as well as analysis and numerics of ordinary and partial differential equations. A group of lecturers, all experts in these fields, will give introductions to different topics.

In the afternoon sessions we will go into detail and learn how to apply the methods in simple Python projects. These Python courses are aimed at students with some prior knowledge of Python, as we cannot offer a basic introduction. Details and more information - especially how to prepare your laptop if you bring your own - are given below.

During the last days of the week we will transition to a workshop character. Experts will present their research in the field of mathematical epidemiology. A call for papers for your contributions of posters and talks is open (see below).

Organizers

Local organizers from Universidad del Valle

• Heliana Arias
• Carmen Ramirez
• Stevens Paz Sanchez
• Olga Vasilieva

Lecturers and complete board of organizers

• Heliana Arias, Universidad del Valle
• Malte Braack, Kiel University
• Dayron Dominguez, Otto von Guericke University Magdeburg
• Carolin Mehlmann, Otto von Guericke University Magdeburg
• Hermann Mena, Max Planck Institute for Dynamics of Complex Technical Systems
• Carmen Ramirez, Universidad del Valle
• Thomas Richter, Otto von Guericke University Magdeburg
• Stevens Paz Sanchez, Universidad del Valle
• Olga Vasilieva, Universidad del Valle
• Thomas Wick, Leibniz University Hannover

Prelimindary Schedule

Monday, December 9

1. 08.30 - 09.20: Registration
2. 09:20 - 09.45: Welcome and Introduction
3. 09.45 - 10:30: Modeling Olga Vasilieva. Wolbachia-based biocontrol for preventing dengue and other mosquito borne human infections.
4. 10:30 - 11:00: Coffee Break
5. 11:00 - 12:00: Analysis Thomas Wick. Brief recap on ODE
6. 12:00 - 14:00: Lunch break
7. 14:00 - 14:45: Numerics Thomas Wick. Solving ODE I
8. 14:45 - 15:00: Break
9. 15:00 - 16:30: Practical Dayron Dominguez. numpy and scipy for solving odes

Tuesday, December 10

1. 09.00 - 10:30: Modeling Hermann Mena. Modeling, Simulation and Control of Vector-Borne Diseases
2. 10:30 - 11:00: Break
3. 11:00 - 12:00: Numerics Thomas Wick. Solving ODE II
4. 12:00 - 14:00: Lunch break
5. 14:00 - 15:00: Numerics Hermann Mena. Scientific Machine Learning and Model Order Reduction for Simulating Vector-Borne Diseases
6. 15:00 - 15:15: Break
7. 15:15 - 16:30: Practical Dayron Dominguez, Hermann Mena. Introduction to pyMOR

Wednesday, December 11

1. 09.00 - 09.45: Invited Talk Paula Castro Autopsy of SARS-CoV-2 spread dynamics in Ecuador using data assimilation techniques
2. 09.45 - 10.30: Analysis Thomas Richter. PDE basics
3. 10:30 - 11:00: Break
4. 11:00 - 12:00: Numerics Carolin Mehlmann. Numerics of PDEs
5. 12:00 - 14:00: Lunch break
6. 14:00 - 15:00: Practical Carolin Mehlmann. PDEs in Python
7. 15:00 - 15:15: Break
8. 15:15 - 16:30: Poster Session

Thursday, December 12

1. 09.00 - 09.45: Invited Talk
2. 09.45 - 10.30: Analysis Thomas Richter. Nonstationary PDE discretization
3. 10:30 - 11:00: Break
4. 11:00 - 12.00: Numerics Thomas Richter. Nonstationary PDE discretization
5. 12:00 - 14:00: Lunch break with
6. 14:00 - 15:00: Discussion Olga Vasilieva. Challenges and open Questions
7. 15:00 - 15:15: Break
8. 15:15 - 16:30 Practical Dayron Dominguez. Solving nonstationary PDEs in Python
9. 19:00 - 23:00: Joint Dinner

Friday, December 13

1. 09.00 - 10.20: Contributed Talks Debora Meideiros An antibody and viral load vector-host dengue fever model
2. 09.00 - 10.20: Contributed Talks Bayron Leon
3. 09.00 - 10.20: Contributed Talks Paulo Amorim Modeling disease awareness and variable susceptibility with a structured epidemic model.
4. 09.00 - 10.20: Contributed Talks Ronal De La Cruz
5. 10:20 - 11:00: Break
6. 11:00 - 11:45: Invited Talk Roxana López Cruz From ODE-PDE to DDE models in Epidemiology
7. 11:45 - 13:00: Closing

Python classes

The Python exercises will be carried on using its powerful ecosystem of scientific computing libraries, including:

• NumPy: For numerical computations and array operations.
• SciPy: For scientific computations, including ODE solvers.
• NGSolve: A tool for solving PDEs with advanced finite element methods.
• PyMOR: A library for model order reduction, particularly useful in solving high-dimensional systems efficiently.

Installing Dependencies

To get started, you need to install the required dependencies for these tools. We provide installation scripts tailored for two different systems:

1. Debian-Based Systems (e.g., Ubuntu)

1. Download the script: deb-installation-summer-school-cali.zip
2. Extract the zip file and ensure the .whl file is in the same folder as the script.
3. Run the scripts, first deb-installation-ode-ngsolve-v3.sh and then deb-installation-PyMOR-v3.sh
4. At the end, Python 3.12, numpy, scipy, matplotlib, ngsolve, the compilers for C++ and Fortran, PyMOR, amount other required scientific computing packages will be installed.

2. Windows Systems

1. Download the script: win-installation-summer-school-cali.zip
2. Extract the zip file.
3. Execute the scripts in a Command Prompt with administrative privileges to install the necessary dependencies. First run the script win-installation-odes-ngsolve.bat and then win-installation-pymor.bat
4. These scripts will install Python 3.12, numpy, scipy, matplotlib, ngsolve, the compilers for C++ and Fortran, conda, PyMOR, amount other required scientific computing packages.

Using JupyterLab for Programming

Throughout this course, we will use JupyterLab as a programming tool. JupyterLab provides an interactive environment for writing and running Python code. We highly recommend installing it in your Python environment. Please, follow the installation instructions of the oficial JupyterLab website.

Important Notes

The provided scripts perform a basic installation of the dependencies. We strongly recommend using Pyenv to manage Python versions and virtual environments (venv, conda, etc. are also available). It allows you to isolate project dependencies and avoid version conflicts or unintended modifications to system-wide packages.

If you're using the Debian-based script, ensure the .whl file for slycot is in the same folder as the script before running it. This is necessary for successful installation.

Fee

A small conference fee may be charged by the local organisers (probably a maximum of USD 20). Details will follow shortly.

Registration and call for papers

The registration to the summerschool and call for abstracts is closed. Please write a mail to thomas.richter@ovgu.de if you are still interested in joining us.

Contact

Thomas Richer at Otto von Guericke University Magdeburg thomas.richter@ovgu.de.