Workshops

We are pleased to announce the 2024 Annual Cell Modeling Online Summer School and Hackathon, which will take place Monday, July 22nd, through Friday, July 26th, 2024. We appreciate your help in letting your colleagues and students know about this opportunity. A flier announcing the workshop is attached.

This year’s workshop will take place over 5 days. The workshop will focus on building cellular models using Tellurium and Roadrunner. The first three days will cover basic modeling techniques. The fourth day will be a special hackathon on the credibility of models, with the last day reserved for special talks. Because our simulation platform uses Python there will be an introductory set of lessons on the first day to get all attendees up to speed.

WHAT YOU WILL LEARN:
By the end of this week-long course, participants will have learned how to use data to build quantitative, predictive chemical network models to test hypotheses and interpret data. The course covers subcellular modeling, which includes metabolic and protein signaling systems. No specific programming or mathematical experience is required.

REGISTRATION:
Please complete this Google Form: bit.ly/2024SumerSchoolRegistration

AUDIENCE:
Mathematical Biologists, Computational Biologists, Experimental Biologists, Medical Scientists, Bioengineers, and Biophysicists, ranging from undergraduates to senior faculty, with a current or potential interest in mechanistic modeling of biological systems. The course covers cellular modeling, which includes budding models of metabolic and protein signaling systems. No specific programming or mathematical experience is required.

AIM AND FOCUS:

• An Introductory Python Tutorial will take place on July 22nd, 2024.
  If you already know Python you may skip this tutorial (or take it as a review).

• Cell Modeling Summer School: Basic Course (July 22nd – July 26th, 2024)
  Mechanistic modeling is an integral part of contemporary bioscience, used for hypothesis generation and testing, experiment design and interpretation, and the design of therapeutic interventions. The Tellurium modeling environment allows researchers to very rapidly build and execute complex network simulations with minimal programming experience. By the end of the course, participants will have had practice in using all the standard features of Tellurium needed to run a variety of simulations.

• Credibility Hackathon (Thursday, July 25th, 2024):
  The hackathon has two objectives:
  (a) aid participants in developing expertise with the modeling tools described earlier in the week, and
  (b) explore the credibility of published biomedical models. The hackathon will be structured as multiple breakout sections, and each breakout will be led by an expert in modeling tools. Participants will analyze models in published papers to assess their reproducibility, understandability, verification, and parameter sensitivity. It is anticipated that these sessions may culminate in publications collaboratively authored by the participants who have distinguished themselves during the breakout sessions.

• Invited Talks
  TBD

CORE TOPICS:

• Principles of modeling biological and biomedical problems
• Python and Antimony scripting
• Cellular modeling with Tellurium/roadrunner (Antimony editor if it’s ready- annotating)

INSTRUCTORS:
Prof. Herbert M. Sauro, University of Washington
Prof. Joseph L Hellerstein, University of Washington
Dr. Lucian Smith, University of Washington
Prof. John Gennari, University of Washington

PARTICIPATION:
Because the number of attendees is limited, admission is by application only. To apply for admission, please register at bit.ly/2024SumerSchoolRegistration.

DEADLINE for APPLICATIONS:
June 28th, 2024. Applications will be processed as received.

The workshop is partially supported by grants from the US National Institutes of Health. Enrollment is free.

We look forward to welcoming you online this July!

Date: July 22-26, 2024

Time (and timezone) breakdown:

9 AM PDT [11 AM CEST | 12 PM EDT] – 4 PM PDT [6 PM CEST | 7 PM EDT]

Schedule

Friday’s Invited Talk Schedule