Developing Multi-Cell Developmental and Biomedical Virtual-Tissue Simulations using CompuCell3D - Tutorial

Saturday, June 14th 2014 , 9:00 - 19:00

ECMTB 2014 Goetheborg, Sweden. Exact Location: To Be Announced

Location : Pascal Auditorium ,Hörsalsvägen 1 Goethenburg, Sweden, (building next to the library at Chalmers University)

See the link for directions/map Pascal Auditorium

Registration:

The tutorial is a part of ECMTB 2014 Conference (www.ecmtb2014.org). We do not require separate registration for CompuCell3D Tutorial but because space is limited we would kindly ask that you send us an email if you intend to attend. This will help us plan better the actual tutorial. We hope to see you there!

Please email Maciej Swat (mswat@indiana.edu) to inform us that you will attend the tutorial

Organizers

• Maciej Swat (Indiana University, Bloomington, IN)
• Roeland Merks (CWI, Amsterdam , Netherlands)
• James Glazier (Indiana University, Bloomington, IN)
• Xiao Fu (Indiana University, Bloomington, IN)

Purpose:

This tutorial will teach participants to develop their own models using CompuCell3D – an open-source, multi-cell, multi-scale environment for biomedical virtual-tissue simulations of development, homeostasis and developmental diseases. CompuCell3D uses an easy-to-comprehend model-description language and most users are able to develop simple CompuCell3D-based simulations after a 30 minute introductory lecture. By the end of the tutorial, participants will be able to build simulations including cell growth, death, motility, differential adhesion, chemotaxis, differentiation and polarization, reaction-diffusion of extracellular chemical fields and finite-element representation of elastic and plastic ECM. As a use case, participants will build simple CompuCell3D simulations of vascularized tumor growth.

Logistics

The tutorial will consist of:

1. A brief introductory presentation on CPM modeling techniques – including an overview of examples of CPM-based simulations.
2. Hands-on tutorials – simple cell sorting models, vascular network formation, cell growth, division, death, and links to subcellular models.
3. User discussion, including how to build realistic vascularized tumor growth simulations as an advanced use case for CompuCell3D.

We encourage users to bring laptops so they can conduct the exercises (For Windows and OSX we provide binary installer packages. Linux, in general, will require CompuCell3D recompilation). Target Audience: Anyone interested in building multi-cell virtual-tissue simulations of development, homeostasis or developmental diseases like cancer. Familiarity with a scripting language like Mathematica, Matlab or Python will be helpful, but not required.

Background Information:

CompuCell3D is a well-supported, open-source environment for building and running multi-cell virtual-tissue simulations based on the Cellular Potts Model (CPM, aka GGH) methodology., which models cell behaviors at the multi-cell level. CompuCell3D also includes biochemical reaction network models at subcellular and inter-cellular scales via BionetSolver (which runs SBML models inside each cell and between cells) and continuum models of tissue mechanics and transport at the tissue level via Partial Differential Equation (PDE) and Finite Element-like methods. While sufficiently simple that a simulation of tens of thousands of cells runs in a reasonable time on a single-processor laptop, CompuCell3D models are detailed enough to allow specification of cell properties like volume, membrane area and cell behaviors like adhesion, chemotaxis, polarization, growth, death and division.

A key feature of CompuCell3D is that users define models using a model-description language, CompuCell3D Markup Language (CC3DML), and open-source Python scripts, rather than hand coding in a low-level language like C++. Consequently, CompuCell3D simulations do not require code compilation. High-level model description reduces the need for detailed knowledge of numerical analysis and programming techniques during model development, and facilitates model validation, publication, sharing and reuse. CompuCell3D significantly reduces the time needed to develop new simulations. Because it is open-source it allows users to examine the base code and enhance, modify and improve it, as needed. CompuCell3D simulations address, among other topics, Age-related Macular Degeneration (AMD), evaluation of radiation-treatment strategies, gastrulation and somitogenesis, Drosophila and vertebrate eye development, limb development, bone regeneration, avascular and vascular tumor progression, angiogenesis and lumen formation and biofilm growth.

Interdisciplinary aspects: CompuCell3D is one of the few multi-cell virtual-tissue simulation platforms that allows rapid development and execution of multi-cell models that link across multiple modeling scales. CompuCell3D is actively developed and updated, allowing researchers representing different modeling scales/domains to collaboratively build and deploy complex biomedical simulations.