CompuCell3D and SBW 11th User Training Workshop

Applications due June 30th, 2017

Workshop Poster

Dear Colleagues,

I would like to invite you to the 12th User Training Workshop, Developing Multi-Scale, Virtual Tissue Simulations with CompuCell3D

July 30th—August 4th, 2017

Indiana University, Bloomington, IN, USA

Background: Mechanistic modeling is an integral part of contemporary bioscience, used for hypothesis generation and testing, experiment design and interpretation and the design of therapeutic interventions. The CompuCell3D modeling environment allow researchers with modest programing experience to rapidly learn to build and execute complex Virtual Tissue simulations of development, homeostasis, toxicity and disease in tissues, organs and organisms, covering sub-cellular, multi-cell and continuum tissue scales. Simulations written using these environments are compact and run on Windows, Mac and Linux, desktops. 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 of their particular biological problem of interest. Post-course support and collaboration will be available to continue 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 your system.

Format: The workshop will include a limited number of lectures and numerous hands-on computer tutorials. Each attendee will also present a mini-talk on her/his problem of interest.

Instructors: Julio Belmonte, James A. Glazier, Andy Somogyi

Target Audience: Experimental Biologists, Medical Scientists, Biophysicists, Mathematical Biologists and Computational Biologists from advanced undergraduates to senior faculty, who have an interest in developing multi-scale Virtual-Tissue simulations, or learning how such simulations might help their research. No specific programming or mathematical experience is required, though familiarity with a modeling environment (e.g. Mathematica®, Maple®, Python, or Matlab®) and how to represent basic concepts like diffusion and chemical reactions mathematically, will be helpful. Important: An Introductory Python Tutorial will take place on July 30th. If you already know Python you may skip this part of the workshop.

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

Application and Registration: Enrollment is limited and by application only. To apply, please send a c.v., a brief statement 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 application materials electronically to Andy Somogyi ( ) by June 30th, 2017.

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

For more information, please contact: Andy Somogyi ( )

Dr. Andy Somogyi

Department of Intelligent Systems Engineering

Indiana University

Bloomington, Indiana 47405


Workshops/Workshop17 (last edited 2017-05-10 15:36:45 by thielmax)