Biomathematics Unit

University of Pennsylvania School of Veterinary Medicine | 382 West Street Road Kennett Square, PA 19348 | Phone: 610.444.5800


BE 567 Modeling Biological Systems


The course presents a comprehensive account of the application of modeling methodology to the investigation of biological systems. The emphasis is on an organized overview of the tools and techniques rather than the detailed mathematical structures upon which they may rely. The course draws examples widely from the current literature in an attempt to not only show the topical relevance of the subject matter but also to equip participants with an understanding of the diversity of domains to which the techniques and methodologies apply. At the center of all systems included pervails the following themes :

  • based on the science surrounding the system what mechanisms are likely to interplay
  • how can we represent those mechanisms in a model
  • how can we corroborate our understanding of the system
  • what are the implications if we are wrong...what are the implications if we are right

Course participants are given ample opportunity during the course to explore, first hand, most of the methods discussed and through team projects and seminars the opportunity to clarify their understanding of the principles and the application of the techniques.

Course Objectives

After completing this course participants will :

  • understand the steps of model formulation
  • appreciate the role modeling has to play within the scientific method
  • be able to use a computing package to investigate the aptness of a model
  • understand the various sources of data underpinning models
  • be able to logically appraise models from both mechanistic and empirical perspectives
  • be able to critically review scientific articles for which key contributions are predicated on models

Topics covered

  • An introduction to simulation modeling
  • Nonlinear systems
  • Linear compartmental systems
  • Computer approaches to modeling nonlinear systems
  • Computer software for modeling compartmental systems
  • Sensitivity and stability analysis
  • Radiolabel experiments with linear systems
  • The investigation of large models
  • Fitting models to experimental data Identifiability


These are some of the lectures and handout materials in Power Point format:

09/07/00 Overview

09/14/00 Lecture 2

09/21/00 Linear Compartmental models: overview

              Handout: Eigenvalue and Eigenvector Determination Made Easy

09/29/00 About Linear Systems as Reflected in Models

10/05/00 The Analysis of Experimental Data