Center for Reproducible Biomedical Modeling

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!

Workshops - Center for Reproducible Biomedical Modeling 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...

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.

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

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.

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

2024 Cell Bio Meeting Dec. 14-18 in San Diego - Center for Reproducible Biomedical Modeling   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