The Center for Reproducible Biomedical Modeling develops workshops alone and in collaboration with several academic organizations and conferences in order to disseminate educational material focused on practical use of modeling software and theoretical explorations of modeling theory. An archive of workshop materials, which includes videos and links to code, data, and model repositories, along with advertisements for upcoming workshops, are maintained below.
2023 1-Day Kinetic Modeling Virtual Course & Hackathon
You are invited to attend a one-day course and hackathon on kinetic modeling with Tellurium! This short course is designed to take beginner and intermediate-level modelers through the main tasks required in a robust kinetic network modeling workflow. The sessions are practical and show attendees how to implement each task with code.
In addition to the practical skills gained in the course, we hope you will expand your professional network and modeling community by connecting with other participants.
You will learn to:
- Write biochemical models using Tellurium and the Antimony modeling language
- Simulate your models with Tellurium and libRoadRunner
- Estimate model parameters
- Perform metabolic control analysis
- Understand case studies from published articles
To register, please fill out this Google Form: https://bit.ly/
Date: July 12, 2023
Schedule
| AM/ PM | Theme | Instructor |
|---|---|---|
| 9 AM – 10 AM PDT | Introduction to biochemical modeling (kinetic models), Python basics, Tellurium and Antimony | Herbert Sauro |
| 10 AM – 11 AM PDT | Michaelis-Menten kinetics, metabolic networks with examples | Michael Kochen and Herbert Sauro |
| 11 AM – 12 PM PDT | Parameter fitting | Joseph Hellerstein |
| 12 PM – 1 PM PDT | Lunch break | |
| 1 PM – 2 PM PDT | Introduction to BioModels and systems biology standards, SBML diagrams | Lucian Smith and Jin Xu |
| 2 PM – 3 PM PDT | Metabolic control analysis | Herbert Sauro |
| 3 PM – 4 PM PDT | Personal project development, open forum (Veronica Porubsky moderates and all instructors contribute) | Veronica Porubsky |
Time (and timezone) breakdown:
9 AM PDT [11 AM CEST | 12 PM EDT] – 4 PM PDT [6 PM CEST | 7 PM EDT]
2023 Network Modeling Summer School & Hackathon
Click photo to download flyer.
