Center for Reproducible Biomedical Modeling

The 26th online Annual Workshop on Computational Cell Biology will take place February 24-28, 2025 at the Center for Cell Analysis and Modeling at UConn Health. The course (the tentative schedule https://compcellbio.org/assets/2025_CCB_online_schedule.pdf) will combine lessons on modeling techniques (e.g. ODE, PDE, stochastic, spatial stochastic, agent- and rule-based modeling) using VCell (http://vcell.org/), COPASI (http://copasi.org/) and SpringSalad (https://vcell.org/ssalad), and interactive hands-on sessions using software to design your models and perform simulations.

There is no registration fee, but please register (https://forms.gle/nPgXDa3A6kXdPTrh7) by January 31st. To be included in the project track, please send 1-2 page proposal explaining how you feel VCell, COPASI and/or SpringSalad will help your research project to Dr. Michael Blinov [email protected]. This info will allow us to determine if the current implementations of our tools apply to your project.
More info is in the attached flyer - please spread the word!

Modeling topics include but not limited to:
• Spatial modeling
• Using ImageJ in spatial modeling
• Parameter Estimation
• Rule-based modeling with BioNetGen & NFsim
• Langevin simulations with SpringSaLaD
• Stochasticity & Discontinuity – Scripting
• Common modeling pitfalls
• Spatial stochastic modeling with SmolDyn

Research talks are given by:
• Aniruddha Chattaraj, Harvard University
• Margaret Johnson, John Hopkins University
• Leslie Loew, University of Connecticut School of Medicine
• Pedro Mendes, University of Connecticut School of Medicine

A separate in-person workshop is being planned for summer 2025 in Farmington, CT. More details to follow.

The Center for Reproducible Biomedical Modeling invites you to join the second speaker of our fall 2024 Building Models and Publishing Models Seminar Series.

Join us on Friday, November 15th as we hear Curvenote CEO from Dr. Rowan Cockett, PhD as he speak on the future of science publishing! Discover how Curvenote enhances interactivity, computation, & reproducibility in scientific work, collaborating with organizations like AGU, MSA, & Physiome. Be part of open science's evolution!

To register for Dr. Cockett's seminar, please visit https://forms.gle/eiCLQ7azirafYNbA7.

You can also visit the CRBM Seminars page to register for other upcoming speakers in the series.

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The virtual begins on Monday! Check out the website for more details:

https://reproduciblebiomodels.org/dissemination-education/2024-cell-modeling-online-summer-school-and-hackathon/



Organized by the Center for Reproducible Biomedical Modeling at the University of Washington Department of Bioengineering.

We are pleased to invite you to participate in the second of two Online Cell Modeling Seminars for the Summer of 2024 organized by the Center for Reproducible Biomedical Modeling and Dr. Herbert Sauro. This seminar will take place on Friday, July 12, 2024.

Presentation: pyPESTO: A Modular and Scalable Tool for Parameter Estimation for Dynamic Models
Date: Friday, July 12, 2024
Time: 4 PM Eastern | 3 PM Central | 1 PM Pacific
Format: 50-minute talk followed by a 10-minute discussion
Platform: Zoom (pre-registration required)*
Register: https://forms.gle/cTUdn478CTg1denFA

Our distinguished speaker, Paul Jost, a Software Developer and Ph.D. student at Universität Bonn, has developed innovative software tools to facilitate dynamical modeling in biological systems. His research focuses on single-cell lipid metabolism, contributing to a deeper understanding of cellular processes.

During this seminar, Paul will showcase pyPESTO, a Python toolbox designed for parameter estimation in systems biology. He will discuss its applications and benefits for researchers, highlighting how it can enhance your research endeavors.

Register Now: To secure your spot in this insightful seminar, please register using the following link: https://forms.gle/cTUdn478CTg1denFA.

A confirmation email will be sent to complete registration for the Zoom seminar.

Don’t miss this opportunity to learn about cutting-edge tools and principles that can significantly benefit your research. We look forward to your participation!

* Those who registered for the June 28th seminar by Pedro Mendes are already registered for this upcoming seminar on July 12th. You may have already received an email notification. All others will need to pre-register.