Modeling Software Platforms

Tuesday, Sept. 3rd, afternoon

Introduction to Tellurium and Related Tools for Systems Biology Modeling

This workshop session is designed for systems biology modelers who wish to leverage the capabilities of Tellurium, a Python-based modeling environment. Participants will be introduced to the basics of Tellurium, including its installation, key features, and applications in systems biology. The session will cover essential concepts such as model construction via the simple Antimony model description language, simulation, and analysis using Tellurium’s intuitive syntax and integrated tools. Attendees will learn how to create models using SBML (Systems Biology Markup Language) and perform time-course simulations, and steady-state analysis. The tutorial will also delve into more advanced topics, such as model fitting, sensitivity analysis, and network visualization. By the end of the session, participants will have hands-on experience in building and analyzing systems biology models, enabling them to apply these skills to their research projects. This session is suitable for beginners with no prior experience in Tellurium, as well as for more experienced modelers looking to enhance their toolset. Some experience with Python is required.

Organizers

Herbert M Sauro, Lucian Smith (University of Washington, Bioengineering, Seattle, USA)

Target Audience

VPH community and modelers in general (keywords: systems and synthetic biology modelers)

Agenda/ Learning Objectives

By the end of this tutorial, participants will be able to:

1. Install and Set Up Tellurium:

– Successfully install Tellurium.

– Navigate the Tellurium environment and its key features.

2. Understand Core Concepts of Systems Biology Modeling:

– Understand how biochemical network models are built.

3. Construct and Simulate Models:

– Create models using Antimony and generating the Systems Biology Markup Language (SBML).

– Execute time-course simulations to analyze dynamic behaviors of biological systems.

4. Perform Model Analysis:

– Conduct parameter scans to explore model behavior under varying conditions.

– Execute sensitivity analysis to identify key parameters influencing model outcomes.

5. Advanced Model Analysis:

– Examine the dynamic stability of some key model configurations.

– Draw network models using the SBML standard and annotate the diagram

6. Describe additional third-party tools that modelers can add to their toolbox

– Recommendations for parameter fitting

– Web-based tools such as makeSBML and the Antimony Web annotation tool

– Network drawing tools such as Alcuin