"Developing Multi-Scale,Multi-Cell Developmental and Biomedical Simulations with CompuCell3D and SBW"
Joint Training Workshop, August 8th-19th 2011, Indiana University, Biocomplexity Institute, Bloomington, IN, USA
Our 5th User Training workshop
Thank you to everyone who attended the Workshop and helped make it possible
Agenda:
CompuCell3D workshop Materials
For SBW Course Materials visit the SBW Course Website
Background:
Modeling is becoming an integral part of contemporary bioscience. The Glazier-Graner-Hogeweg (GGH) model as implemented in the modeling environment, CompuCell3D allows researchers to rapidly build complex models of multi-cell processes in development and disease with user-selectable resolution, from sub-cellular compartmental models to continuum models of tissues. To efficiently link to sub-cellular scale users build biochemical reaction models using SBW and use exported models in the SBML format to control properties of simulated cells in CompuCell3D. CompuCell3D and SBW are simulation environments that target complementary areas of biological modeling. By combining the capabilities of both frameworks users can build truly multi-scale models of tissues, organs or organisms with minimal amount of hardcoded, heuristic rules. CompuCell3D and SBW are open source, allowing users to extend, improve, validate, modify and share the core software.
Goal:
By the end of the two week course, participants will have implemented a basic simulation of the particular biological problem they work on. Post-course support and collaboration will be available to continue simulation development.
Topics:
Introduction to Reaction-Kinetics (RK) models. Introduction to SBW, Simulation, Network design tools and SBML. Introduction to GGH modeling. Applications of GGH modeling. Introduction to CompuCell3D. Python scripting. Basics of model building. Extending CompuCell3D. Building a basic simulation of your system.
Workshop Poster: WorkshopPoster_2011.pdf