Tutorial 8

8/30 12:15 - 2:45, Hewlett 201

Systems Biology Workbench

Frank T. Bergmann1,2 and Kyung Hyuk Kim1

1.Department of Bioengineering, University of Washington. 2.Keck Graduate Institute.

This tutorial aims to familiarize participants with the tools provided in the Systems Biology Workbench for building and analyzing deterministic and stochastic models. Using SBW and integrated 3rd party software, we will introduce modeling, time course and steady state concepts, parameter sensitivity (MCA) and bifurcation analysis. The Systems Biology Workbench (SBW) is an extendable, open source software framework, connecting software applications written in a variety of programming languages. Software components provided with SBW assist in analyzing, creating, optimizing, simulating and visualizing computational models. Tutorial Outline (tutorial length is approximately 3 hours):

  1. Introduction to the Systems Biology Workbench (15 minutes)
    • The framework
    • The modules
  2. Modeling (30 minutes)
    • Brief Introduction to modeling
    • Continuous vs. stochastic modeling
    • Script based modeling using Jarnac
    • Modeling in the visual environment JDesigner
  3. Simulation / Visualization (10 minutes)
    • Time course analysis
    • Steady state analysis
  4. Break (10 minutes)
  5. Hands-on Exercises (25 minutes) - Homeostasis, feed-forward networks and MCA
  6. Analysis (20 minutes)
    • Hands-on Exercises - Feedback Oscillators
    • Bifurcation Analysis using the Bifurcation Discovery Tool and Oscill8 and Auto.NET.
    • Frequency Analysis
  7. Break (10 minutes)
  8. Stochastic simulation and analysis (15 minutes)
    • Stochastic focusing, cell fate decisions and stochastic switching
    • Approaches to analyzing stochastic simulation data
  9. Hands-on Exercises (25 minutes) - Stochastic reaction networks
  10. Discussion (15 minutes) a. Future Directions and Q & A
The target audience for this introductory tutorial will be research scientists and students interested in modeling as well as simulation and analysis of computational models. Participation in the tutorial does not require prior experience in modeling/simulation or skills in computer programming. Tutorial material along with a software release will be made available on http://sys-bio.org. If you require further information, please do not hesitate to contact Frank Bergmann at fbergman@u.washington.edu.

Registration Registered attendees please register for this Tutorial.