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

Do you have early-career members (post-doc, assistant to newly associate professor level, research and tenure track) in your organization that would benefit from a novel, interdisciplinary opportunity to collaborate?  Please encourage them to apply for the 2019 Data Science Innovation Lab: “Data Science Challenges in Rural Health and Environmental Exposures” taking place June 24th-28th, 2019 at the Graylyn International Conference Center in Winston-Salem, NC.

Meeting Date:
Monday, June 24, 2019 to Friday, June 28, 2019
Meeting Location:
Winston-Salem, NC

Machine Learning in Neuroscience: Fundamentals and Possibilities

Organized by Kristin Branson and Edda “Floh” Thiels

June 26, 11 a.m.–5 p.m. EDT

Meeting Date:
Wednesday, June 26, 2019
Meeting Location:

The Society for Mathematical Biology promotes the development and dissemination of research at the interface between the mathematical and biological sciences through its annual meetings. The Annual Meeting of the Society for Mathematical Biology is the most important event organized and sponsored by the Society. It is the most visible yearly event organized by the Society and hence serves as a show case for the goals, ambitions and activities of the society.

Meeting Date:
Monday, July 22, 2019 to Friday, July 26, 2019
Meeting Location:
Montreal, Canada

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