Welcome to CompuCell3D
Mac Security Problem
If you are using Mac OS 10.15.x you may have problems running CompuCell3D because of Apple's increasingly onerous security measures. If you encounter problems please contact us at <jsluka AT Indiana DOT edu>.
Call to Contribute: Collaborative Tissue Model Development to Mitigate the Coronavirus Pandemic
The rapidly evolving social and medical impact of COVID-19 requires equally rapid development of tools to predict, and ultimately ameliorate, the future course of the pandemic. Tools are needed to predict patient outcomes, to optimize the deployment of resources by medical providers, and to optimize therapy for infected individuals. Predictive computational simulations of the spread of the disease, and of the underlying biology that makes COVID-19 unique, are both essential. Our aim is to build cooperatively-developed, open-source multiscale model components that can predict various aspects of infection at molecular and tissue scales and inform higher-level models, and a framework to allow others to do so efficiently.
COVID-19 Model Repository: Because of the urgency of the crisis, software development must be done in parallel and not sequentially as in normal scientific model development. As such, we are developing a model repository for the cooperative development of public, open-source molecular- and tissue-scale models and simulations of various infection events and health states associated with COVID-19. To support rapid parallel development, integration, and sharing of models and simulations, we are developing modeling and simulation tools specific to this project, as well as documentation tools and standards for rapid and consistent dissemination of repository contents. Please join us in our efforts to collectively mitigate the ongoing pandemic and future pandemics alike on GitHub. For more information, please contact us at <tjsego AT iu DOT edu>.
Model of Viral Tissue Infection: In support of parallel model development of tissue infection, the members of the Biocomplexity Institute are developing a multiscale computational model of viral tissue infection using CC3D. The model describes select interactions between generalized epithelial and immune cells and their extracellular environment associated with viral infection and immune response at the cellular and intracellular levels, and in the context of spatiotemporal dynamics. The model is a generic viral infection model, and our hope is to collaboratively develop it into a model of SARS-CoV-2 tissue infection and Covid-19 progression. As such, it is intended to serve as a base model for constructing and implementing more advanced models of targeted cellular- and intracellular-level phenomena in tissue after initial exposure. In its current state, it has not been formally peer-reviewed, and should not be used for patient diagnostics or predicting clinical outcomes. Rather, the model and its implementation can be used to develop and interrogate mechanistic hypotheses about the spread of a virus and how the interplay between viral spreading and immune response determine the outcome of the disease, such as:
- Why does the progression of the disease seem to be dependent on the initial viral exposure level?
- Why is the start time of symptoms and immune response so variable?
- What is the role of cytokine signaling in explaining immune response variability?
Model documentation and simulation files can be found in the project folder of our COVID-19 Model Repository. Please be advised that this is a rapidly evolving project, so model and simulation features are subject to change (even daily). For more information about how to contribute to, modify, or reuse the model and simulation, please contact us at <tjsego AT iu DOT edu>.
For information on recent modeling and repository developments, current development plans, and opportunities to contribute to current modeling and repository projects, please see our project page.
CompuCell3D 15th User Training Workshop!
Cellular and Network Modeling:
(click the images to download full size versions of the posters)
July 27th - August 8th, 2020, Bloomington Indiana USA
Network Modeling Summer School (Monday-Thursday, July 27-July 30, 2020) and Hackathon (Friday-Sunday, July 31-August 2, 2020): Covers both basic and more advanced issues for using dynamic models of biological networks. Includes basic concepts of chemical reaction, signaling and gene regulatory networks, stability and sensitivity analysis and deterministic and stochastic modeling. The Tellurium modeling environment allows the specification and execution of network models as part of simple Python scripts, making it flexible and easy to integrate with data analysis and other modeling tools.
Multicell Virtual-Tissue Modeling Summer School (Monday-Thursday, August 3-August 6, 2020) and Hackathon (Friday-Sunday, August 7-August 9,2020): 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 programing 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. Virtual-Tissue simulations developed using CompuCell3D run on Windows, Mac and Linux. CompuCell3D is open source, allowing users to extend, improve, validate, modify and share the core software.
Format: The Summer Schools will include a limited number of lectures and numerous hands-on computer tutorials. There will be breakout sessions for basic and advanced modelers.
In the hackathons, attendees will be grouped into teams based on topic of interest. Each team will include experienced modellers. The teams will each build a functioning core model, which each participant can further customize. Advanced modelers can apply to attend just the weekend hackathons.
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.
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 be offered on July 26th, 2020. If you are already familiar with Python basics, you may skip this tutorial or attend for review.
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.
Online Participation: The summer schools will support online participation through Zoom.
Registration: Click here to Register!
CompuCell3D on nanoHub!
CompuCell3D 3.7.6 is available for online use on nanoHUB. Some CompuCell3D simulations are already available as tools (for example: Vascular Tumor, Cell Sorting). If you have a request or suggestion for a new simulation to be deployed in nanoHUB please go to our suggestion thread in our support forums, here. If you have a CompuCell3D simulation that you want to deploy on nanoHUB please see this github repository.
***NEW*** CC3D Version 4.1.1
We are pleased to announce new version 4.1.1 of our software CompuCell3D.
Important Because we switched from Python 2 to Python 3 your old simulations will require minor modifications Please see https://pythonscriptingmanual.readthedocs.io/en/4.0.0/transition_to_cc3d_4.html for instructions on how to port your simulations. If you have questions or require assistance please reach out to use on our user support forum https://www.reddit.com/r/CompuCell3D/
Important We suggest that as you move to CC3D 4.0.0+ you keep old installation of CC3D (version 3.7.x) in place in order to ensure that you can run your simulations during transitions period. CompuCell3D 4.0.0+ stores settings in different place from earlier version so you can safely run new and older versions side-by-side.
- Added support for specifying Reaction-Kinetics models in Antimony and CellML (Windows and OSX)
- Fixed parameter scan to allow runs with multiple workers
- Added callable API allowing CC3d to be called as a function returning values
- Fixed restart files issue
- Fixed PIFF dumper
- Fixed hover over text in Player
- Added support for developing custom C++ steppables and plugins on OS
- Expanded compilation documentation for all 3 platforms
- Improved data passing between steppables
- Added optional comments in code snippets
- Improved interface with fpp plugin and new accessible plugin data in steppables
Added access to BoxWatcher data in steppables
- Fixed domain resizing
CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D's intuitive interface makes Virtual Tissue modeling accessible to users without extensive software development or programming experience.
It uses Cellular Potts Model to model cell behavior. Below is a preview of what CC3D can do:
This project is currently funded by generous support from the U.S. National Science Foundation (NSF) grant NSF-1720625, “Network for Computational Nanotechnology - Engineered nanoBIO Node” and by the National Institutes of Health (NIH) grant NIH - R01 GM122424, “Competitive Renewal of Development and Improvement of the Tissue Simulation Toolkit”. Information on previous support is listed on our Support page.
CompuCell3D is led by James A. Glazier (Indiana Univ) in collaboration with Dr. David Umulis (Purdue Univ). Many people contribute, or have contributed, to CC3D including the original lead developer Maciej Swat.
New CC3D forum
To report any bugs, or to ask questions, please visit our Q&A page: Reddit CompuCell3D.
Note: In April 2019 our old user forum at CC3D - AllAnswered was discontinued. The entries in the old AllAnswered forum are available at CC3D AllAnswered archive.html. The text of the questions and answers are there but the linked files are not. If you need one of the linked files please ask for it on the Reddit forum.
Want to contribute to CompuCell3D development?
We highly encourage fellow researchers to contribute to CompuCell3D code. If you have developed some useful plugin or functionality on CompuCell3D and would like share it with rest of us. Please commit the code and open a pull request on CompuCell3D GitHub repository. We would love to see it in next version of CompuCell3D.
Have CompuCell3D-related Question?
How to cite CompuCell3D
Multi-Scale Modeling of Tissues Using CompuCell3D – M. Swat, Gilberto L. Thomas, Julio M. Belmonte, A. Shirinifard, D.Hmeljak, J. A. Glazier, Computational Methods in Cell Biology, Methods in Cell Biology 110: 325-366 (2012). PMID:22482955 PMCID: PMC3612985 DOI: doi.org/10.1016/b978-0-12-388403-9.00013-8