User Training Workshop Developing Multi-Scale, Virtual Tissue Simulations with CompuCell3D

Mechanistic modeling is an integral part of contemporary bioscience, used forhypothesis generation and testing, experiment design and interpretation and the design of therapeuticinterventions. The CompuCell3D modeling environment allow researchers with modest programingexperience to rapidly build and execute complex Virtual Tissue simulations of development,homeostasis, toxicity and disease in tissues, organs and organisms, covering sub-cellular, multi-celland continuum tissue scales. Virtual Tissue simulations developed using CompuCell3D run onWindows, Mac and Linux. CompuCell3D is open source, allowing users to extend, improve, validate,modify and share the core software. For more information please visit:

Goal: By the end of this one-week course, participants will have implemented a basic simulation oftheir particular biological problem of interest. Post-course support and collaboration will be available tocontinue simulation development.

Topics: Python scripting. Introduction to Reaction-Kinetics (RK) models. Introduction to SBML.Introduction to Virtual-Tissue simulations. Introduction to CompuCell3D. Basics of model building.Combining RK and Virtual-Tissue models. Extending CompuCell3D. Building a basic simulation of yoursystem.

Format: The workshop will include a limited number of lectures and numerous hands-on computertutorials. Each attendee will also present a mini-talk on their problem of interest. There will beconcurrent sessions for basic and advanced modelers.

Instructors: James A. Glazier (Indiana University), Julio Belmonte (North Carolina State University),Maciek Swat, Juliano Gianlupi (Indiana University), Andy Somogyi (Indiana University), James Sluka (Indiana University).

Target Audience: Experimental Biologists, Medical Scientists, Biophysicists, Mathematical Biologistsand Computational Biologists from advanced undergraduates to senior faculty, who have an interest indeveloping multi-scale Virtual-Tissue simulations, or learning how such simulations might help theirresearch. No specific programming or mathematical experience is required, though familiarity with amodeling environment (e.g. Mathematica®, Maple®, Python, or Matlab®) and how to represent basicconcepts like diffusion and chemical reactions mathematically, will be helpful. Note: An Introductory Python Tutorial will take place on August 11th. If you already know Python, youmay skip this part of the workshop.

Fees: There is no registration fee. We will provide coffee, tea, lunch, snacks and workshop materials.

Registration: Enrollment is limited and by application only. Kindly apply online with a c.v., a briefstatement describing your current research interests and the specific problem you would like to model.Students should also include a letter of support from their current advisor. Please submit all applicationmaterials electronically at by June 10, 2019.

Facilities: The workshop will be held at Indiana University, Bloomington, IN, USA. The nearest airportis Indianapolis, IN. Participants will be able to connect to the Internet using their own laptops.

For more information, please contact: CompuCell3D Team (

2019 IMAG Multiscale Modeling Consortium (MSM) Meeting

MSM Meetings

The National Institute for Mathematical and Biological Synthesis (NIMBioS) is now accepting applications for its Investigative Workshop, "Transients in Biological Systems," to be held May 29-31, 2019, at NIMBioS.Objectives: Transients, or non-asymptotic dynamics, cover a wide range of possibilities, from biology to ecology and beyond. A full understanding of transients and their implications for biology requires mathematical and statistical developments as well as attention to biological detail.

Meeting Date:
Wednesday, May 29, 2019 to Friday, May 31, 2019
Meeting Location:
NIMBioS at the University of Tennessee, Knoxville

Workshop at the Isaac Newton Institute on uncertainty quantification in cardiac modeling: The Fickle Heart
13th May 2019 to 7th June 2019, Cambridge University
Organizers: Steven Niederer (King's College London); Helen Byrne (University of Oxford); Colleen Clancy (UC Davis); Richard Clayton (University of Sheffield); Gary Mirams (University of Nottingham); Ian Vernon (Durham University)


Meeting Date:
Wednesday, June 5, 2019 to Friday, June 7, 2019
Meeting Location:
Cambridge University or remotely

Multiscale Modelling and Simulation Workshop 2019

Meeting Date:
Wednesday, June 12, 2019 to Friday, June 14, 2019
Meeting Location:
Faro, Portugal

This wiki contains information relevant to the IMAG (Interagency Modeling and Analysis Group) and the MSM (Multi-scale Modeling Consortium)Questions about IMAG and the MSM Consortium can be directed to