Goal:

By the end of this two-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 their problem of interest. There will be concurrent sessions for basic and advanced modelers.

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.

Note: An Introductory Python Tutorial will take place on August 11th. If you already know Python, you may skip this part of the workshop.

Fees:

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

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.

Registration:

Click here to Register!

1. biology
2. compucell
3. CompuCell3D
4. python
5. tool:compucell3d
6. workshop