Tools and Examples for Dynamic Modeling in Biology

Agent-based modeling

• AgentSheets
  • $100 for academic version
  • Extremely intuitive interface with drag-and-drop behavior editing
  • Models can be saved as Java applets that run in a browser (without the AgentSheets software)
  • Not easy to create complicated models
• NetLogo
  • Free
  • More flexible and powerful than AgentSheets
  • Thorough online documentation
  • Installs with 400+ pre-built, and documented models (many more user contributed models online, though of mixed quality)
  • Also saves models as applets that run in the browser
  • Major difference from AgentSheets is that models are built by writing code in the Logo language
  • Some NetLogo example models

• CellDesigner - the current version (4.1) of this software links with the SABIO-RK database of reaction kinetic parameters, as well as the BioModels and the Panther Pathways database
• MatLab Simbiology
• Vensim
  • Personal Learning Edition (PLE) is free
  • Build model as box-and-flow diagram, then add quantities and formulas and simulate
  • Some Vensim example models
• Stella
  • Formerly free software, now $650 for academic version ($200 for pre-college educators)

High-level modeling languages

• MatLab
  • MatLab is NOT free, but it's as comfortable as your favorite blanket
  • There are, however, two open source softwares that are similar to the basic command line mode of Matlab. They are:
    • Octave
    • SciLab
    As with other open-source software, these packages are free and very capable. What you are giving up in not paying the MatLab license fee, is: a dedicated support organization, regular user interface and product improvements, and content demonstrating features and applications. THose things are worth something. Whether they are worth the price of MatLab is for you, and your institution to decide.
  • Matlab resources
    • Material for Ohio U. Intro to Bioinformatics course
• R
  • R is totally free, and comfortable to those that don't need a wubby anymore
  • There are currentl over 2000 user contributed packages

Modeling Textbooks

• Introductory
  • Introduction to Computational Science: Modeling and Simulation for the Sciences by Angela B. Shiflet, George W. Shiflet. The authors site for this text includes tutorials and examples for a number of different computational tools.
  • Mathematical Models in Biology: An Introduction by Elizabeth Spencer Allman, John Anthony Rhodes. The publishers site for this text provides MatLab scripts for many of the examples in the text.
  • Biological Modeling and Simulation: A Survey of Practical Models, Algorithms, and Numerical Methods by Russell Schwartz
  • Dynamic Models in Biology by Stephen P. Ellner, John Guckenheimer. The authors site for this text provides MatLab and R scripts for many of the examples in the text.
  • Stochastic Modelling for Systems Biology by Darren James Wilkinson. The authors site for this text provides R scripts and other computing related resources for text.
  • Modeling Biological Systems: Principles and Applications by James W. Haefner.
• Topic Specific