Center for Reproducible Biomedical Modeling

07/17/2025

You are invited to attend a two-day course 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

Time (and timezone) breakdown:
9 AM PDT [11 AM CDT | 12 PM EDT] – 4 PM PDT [6 PM CDT | 7 PM EDT]

For more information and registration, please see our attached flyer or visit: https://reproduciblebiomodels.org/dissemination-training/workshops/

Please share this with colleagues and students you think may be interested!

REGISTRATION:
Enrollment is free.

DEADLINE for REGISTRATION:
July 22nd, 2025.

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

We look forward to welcoming you online this July!

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...

07/01/2025

COMBINE 2025 – Madison, WI

The Computational Modeling in Biology Network (COMBINE) will host its 2025 workshop-style event at the University of Wisconsin-Madison this October.

Location: Pyle Center, UW-Madison (702 Langdon St.), within walking distance to hotels, downtown, and scenic Lake Mendota.

Event Highlights:

• Breakout sessions on COMBINE standards, tools, and applications

• Opportunities to present lightning talks (5 min max.) and posters

• Tutorials and discussions on emerging needs in systems and synthetic biology

• Networking with experts and the broader COMBINE community

Topics of Interest Include:

• Data exchange & modeling standards

• Visualization and graphical notation

• Standards for pathway data & biological models

• Metadata, semantic annotations & AI standardization

• Model & data management across biology fields

• New efforts in multicellular & microbial community modeling

More details and registration, visit https://co.mbine.org/events/

01/10/2025

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 blinov@uchc.edu. 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.

12/06/2024

The Center for Reproducible Biomedical Modeling at the University of Washington Department of Bioengineering invites you to join us on Friday, December 13th, for a talk by Dr. Anna Niarakis, the fourth speaker in our Fall 2024 "Building Models and Publishing Models" Seminar Series.

To register for Dr. Niarakis's seminar, please complete this registration form https://forms.gle/iaR39eDaAs5aYjre8.

Title: Inference of Large-Scale Boolean Models from Human-Curated, Fully Annotated Process Description Diagrams. Focus on Rheumatoid Arthritis

Dr. Anna Niarakis, Ph.D.
Professor of Computational Systems Biology
University of Toulouse III-Paul Sabatier

Friday, December 13, 2024
12 PM | Eastern
11 AM | Central
9 | AM Pacific
6 PM | Toulouse, France

Dr. Anna Niarakis, Professor of Computational Systems Biology at the University of Toulouse III-Paul Sabatier, specializes in complex human diseases, with a focus on autoimmune disorders. Her talk, "Inference of Large-Scale Boolean Models from Human-Curated, Fully Annotated Process Description Diagrams. Focus on Rheumatoid Arthritis," will introduce CaSQ, a tool developed to transform static molecular interaction maps (MIMs) into dynamic Boolean models. By converting detailed, annotated maps into standardized, interoperable models, Dr. Niarakis’s work aims to enhance understanding and reproducibility in disease modeling, with applications demonstrated in Rheumatoid Arthritis research.

12/06/2024

The Center for Reproducible Biomedical Modeling at the University of Washington Department of Bioengineering invites you to join us on Wednesday, December 11th, for a talk by Dr. Jacky Snope, the third speaker in our Fall 2024 "Building Models and Publishing Models" Seminar Series.

Title:
On steroids! Modeling 11-Oxygenated Androgen Levels in Chronic Kidney Disease

Wednesday, Dec. 11th
2 PM | Eastern
1 PM | Central
11 AM | Pacific
9 PM | Stellenbosch South Africa

Dr. Snoep is Stellenbosch University SARChI research professor on Mechanistic modeling of health and epidemiology.

To register for Dr. Snoep's seminar, please complete this registration form https://forms.gle/xWB1HoveYpMJ7EEU9.

Mathematical models are important tools for a quantitative understanding of biological systems. If they are based on biochemically realistic mechanisms they can make predictions on system dynamics in terms of the characteristics of their components. Modeling the healthy and diseased states can give indications on how to intervene and correct the diseased state.

Professor Jacky Snoep is a leading researcher at Stellenbosch University, specializing in mechanistic modeling of health and epidemiology. He is actively engaged in Computational Systems Biology, focusing on metabolic modeling in various disease states, including malaria and type 2 diabetes. Dr. Snoep will illustrate the combined experimental and modeling approach for steroid metabolism in chronic kidney disease and polycystic o***y syndrome. The focus will be on the modeling workflow across biological organization levels: molecules → enzymes → pathway → tissue → whole body modeling in patients.

***ysyndrome

11/07/2024

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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11/05/2024

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

We are excited to kick off the first of our four seminars with Dr. Peter Hunter, FRS, FRSNZ, former Director of the Auckland Bioengineering Institute.

Dr. Hunter’s talk, "Using Bond Graphs to Ensure Thermodynamic Consistency in Biophysical Models," will discuss how bond graphs provide a simple way to ensure that models of biological processes obey the conservation laws of physics (conservation of mass, conservation of charge and conservation of energy). Dr. Hunter will explain bond graphs and discuss how they are used for multi-scale modeling of physiological systems that involve energy transfer between biochemical, electrical, mechanical and thermal mechanisms of energy transmission and storage.

To register for Dr. Hunter's seminar, please visit https://forms.gle/PQw3RLA7TPqBzExs9.

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

Please share this invitation with colleagues who may be interested in attending.

08/09/2024

Don't miss the 2024 Cell Bio Meeting Dec. 14-18 in San Diego! 🌟 Join global leaders in cell biology for networking, cutting-edge research, and innovation. Register now!

https://reproduciblebiomodels.org/2024-cell-bio-meeting

  You are invited to Cell Bio 2024 - an ASCB | EMBO meeting, the joint meeting of the American Society for Cell Biology (ASCB) and European Molecular Biology Organization (EMBO), which will showcase a diverse global community of the brightest minds in cell biology. Come

08/09/2024

"Join us at the 2024 IMAG/MSM Consortium Meeting (9/30-10/2) to explore the future of Biomedical Digital Twins! Let's innovate and collaborate to redefine healthcare. Don't miss out! 🌟

https://reproduciblebiomodels.org/2024-imag-msm-meeting/ "

Join the 2024 IMAG/MSM meeting, where we are pioneering the future of Biomedical Digital Twins (BDT)! The meeting aims to create a community of expertise from academia, industry, medicine, and government to promote, empower, and facilitate the understanding, collaboration, and creation of tools and....

07/19/2024

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.

07/09/2024

We are excited to announce the latest edition of the CRBM Newsletter is now available! Vol. 3: Outreach, Dissemination and Education is packed with insightful articles, updates, and advancements in the field of reproducible bio models.

Here’s a sneak peek of what you’ll find in our latest volume, Outreach, Dissemination, and Education.

OUTREACH
Discover how our center promotes reproducibility and reusability in biomedical modeling through various educational and promotional efforts.

DISSEMINATION
Learn about our innovative tools, methodologies, and the many ways we share our work, including seminars, meetings, and this very newsletter.

UPCOMING SEMINARS AND EVENTS

• Data Use in Systems Biology: FAIR Principles and Applications: Pedro Mendez and Paul Jonas Jost discuss data use and reproducibility in systems biology. Register here by Wednesday, July 10th! https://reproduciblebiomodels.org/dissemination-education/seminar/

• 2024 Cell Modeling Online Summer School and Hackathon: Join us from July 22-26 for an immersive experience with experts like Herbert Sauro and Lucian Smith, culminating in a hackathon on model credibility. Register here by Monday, July 15th. https://reproduciblebiomodels.org/dissemination-education/2024-cell-modeling-online-summer-school-and-hackathon/

• COMBINE Meeting: Join us in Stuttgart, Germany, from September 1-5 for discussions on computational modeling standards and tools. Register here by August 7th.
https://co.mbine.org/events/


HIGHLIGHTS AND UPDATES

• Vivarium: Explore our advancements in integrative multiscale modeling with Vivarium.

• BioModels SED-ML Update: Discover our efforts to enhance reproducibility with updated SED-ML files for the BioModels database.

• SBMLNetwork and Alcuin: Learn about our new tools for visualizing and editing biological models.


QUICK TUTORIALS

• bnglViz: Visualize rule-based models with our web tool for enhanced understanding and presentation.

• MolClustPy: Characterize multivalent biomolecular clusters using our Python package for stochastic simulations.

For detailed articles and more information, read any of our newsletters on our website ( https://reproduciblebiomodels.org/center-newsletters ) and join us in celebrating the remarkable strides being made in our field. Your feedback and contributions are always welcome as we continue to build a vibrant and supportive community.

Thank you for your continued support and engagement. Together, we are advancing the frontiers of reproducible bio models.

In order to ensure that the tools and educational materials developed by the Center for Reproducible Biomedical Modeling are made findable and accessible, a quarterly newsletter on advances in reproducible modeling is distributed to the broader modeling community. The Center for Reproducible Biomedi...

07/03/2024

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.