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 the 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, is maintained below.

2020 Network Modeling & Virtual Summer School
2021 Network Modeling & Virtual Summer School
2022 Network Modeling & Virtual Summer School
2023 Harmony Conference
2023 Kinetic Modeling Virtual Course & Hackathon

2023 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/metabolic_modeling_1_day_course

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.

2023 Kinetic Modeling Virtual Course & Hackathon Archive

Part 1 & Part 2 – Combined
Herbert Sauro & Michael Kochen

July 12, 2023

Parameter Fitting
Joseph Hellerstein

July 12, 2023

Introduction to BioModels and Systems Biology Standards, SBML Diagrams
Lucian Smith and Jin Xu

July 12, 2023

Metabolic Control Analysis

Herbert Sauro

July 12, 2023

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