Course: Multi-Agent Models in Biomedical Simulation


Multi-Agent Models in Biomedical Simulation

Lingua del seminario:



John H, Holmes, PhD
University of Pennsylvania
Perelman School of Medicine, Philadelphia – USA

Resources Schedule Venue Registration

Course Description:

Course description
In this three-day short course, we will develop agent-based models for simulating a variety of
biomedical problems. We will be using the NetLogo software package, which is in extensive use in
agent-based modeling of a very wide variety of domains, not solely biomedical. NetLogo supports an
intuitive graphical interface that allows the user to change parameters that have been specified by a
developer, as well as a programming language (based on Logo, and early entry into the game
programming market). Although NetLogo will be used for purposes of creating the models, we will
also introduce the theory of agent-based and complex systems as well as a process for modeling
agent-based models that has a seamless development pipeline from initial specification of a problem
domain through the implementation of a model.

Learning objectives for the course
1. Demonstrate familiarity with the theory of agent-based models and complex adaptive
2. Show intermediate- to advanced-level of competency with developing and using an agent-
based model implemented in NetLogo
3. Describe uses of agent-based models in biomedical domains

Class format
Each class is three hours in length. The course is designed as a lecture-laboratory, with guided in-
class exercises to illustrate topics covered in the lecture, as they are covered. We will also discuss
one paper each day, that illustrates the use of an agent-based model in a biomedical domain.

Course Resources:

Suggested textbook:
Railsback S and Grimm V: Agent-Based and Individual-Based Modeling: A Practical
Introduction. Princeton, New Jersey: Princeton University Press, 2012. Although not required
for the course, this is one of the best textbooks on ABMs and guides to NetLogo available!
Journal papers: As noted in the Course Schedule and distributed before the course begins.
• NetLogo download page:
o Download the Desktop App, not NetLogo Web!
o The software includes a comprehensive user manual, accessible from the Help menu.)

Course Schedule:

11 June: General Introduction to agent-based modeling and NetLogo

Course overview and introduction
• Agent-based modeling
• The NetLogo platform
• Example: AIDS
Creating an ABM with NetLogo
• The ODD modeling framework
• The NetLogo programming language
Example: AIDS model, found in the NetLogo Models Library: Sample Models/Social Science
Exercise: Implementing a simple model: Ants
Reading: Chiaccio F, et al.: Agent-based modeling of the immune system: NetLogo, a
promising framework. BioMed Research International, Article ID 907171, 2014.

12 June: Contagion and infectious disease modeling

Model design concepts I
• Emergence
• Observation
• Sensing
• Adaptive behavior
Model design concepts II
• Prediction
• Interaction
• Scheduling
• Stochasticity
• Collectives
Exercise: Simulating an influenza outbreak using a common contagion model
Reading: Cooley P, et al.: The role of subway travel in an influenza epidemic: A New York City
simulation. Journal of Urban Health: Bulletin of the New York Academy of Medicine 88(5):982-
994, 2011.

13 June: Built-environment interactions

Pattern-oriented matching
• Patterns for model structure
• Theory development
• Parameterization and calibration
Model analysis and course wrap-up
• Analyzing and understanding agent-based models
• Sensitivity, uncertainty and robustness
• What next?
Example: Pollution model, found in the NetLogo Models Library: Sample Models/Urban Suite
Exercise: Environmental modeling with NetLogo
Reading: Yang Y and Diez-Roux AV: Using an agent-based model to simulate children’s
active travel to school. International Journal of Behavioral Nutrition and Physical Activity
10(67): 1-8, 2013

Course Venue:

More details to be disclosed soon