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: www.compucell3d.org.
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 https://goo.gl/forms/lGMPVFrjhHZFyGdJ3 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 (firstname.lastname@example.org).