13th User Training Workshop
Developing Multi-Scale, Virtual Tissue Simulations with CompuCell3D
August 5th - August 11th, 2018
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 allows researchers with modest programming experience to rapidly 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 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: www.compucell3d.org
Goal: By the end of this one-week course, participants will implement virtual-tissue models combining molecular network, multi-cell and tissue-level model components. Advanced CompuCell3D users will have an opportunity to develop models for their biological problems of interest and learn how to extend and use CompuCell3D to conduct uncertainty quantification. Post-course support and collaboration will be available to continue simulation development for all participants.
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. There will be concurrent sessions for basic and advanced modelers.
Instructors: Herbert Sauro (University of Washington), James Glazier (Indiana University), Gilberto Thomas (UFRGS), James Sluka (Indiana University), Anwar Shaikh (Indiana University), Maciek Swat (CC3D Developer)
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.
Schedule: Sunday, August 5th: Optional introduction to Python | Monday-Friday, August 6th to 10th: Main workshop | Saturday, August 11th: Optional one-on-one session for model development.
Fees: There is no fee. We will provide coffee, tea, lunch, snacks and workshop materials.
Registration: Enrollment is limited and by application only. Kindly apply online with a CV, 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 at http://www.compucell3d.org/register2018 by June 10, 2018.
Facilities: The workshop will be held at Indiana University, Bloomington, IN, USA. The nearest airport is 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).