Welcome to CompuCell3D


All CC3D Modelers are Invited to Our First CC3D Hackathon!

Friday August 7th - Sunday August 9th 2020, 11AM EDT to 6PM EDT each day

We will have a hackathon for anyone interested in developing models (or perhaps new modules or tools) using CompuCell3D. We will break into groups based on participants interests, for example "COVID-19 modeling" or "ECM modeling". For more info visit the Hackathon 2020 page!


REMINDER: Second part of CompuCell3D Multiscale Workshop 2020 has started!

Make sure to join our Zoom sessions and our workshop Slack.

Starting Friday (Aug/07) through Sunday (Aug/09) we will have a hackathon to help you create your models on CompuCell3D! You don't have to have participated in the workshop during the week to join us!

You can watch the introductory python Lectures with Andre Somogyi on YouTube.

Past lectures are available on CompuCell3D's YouTube channel. The days are organized into playlists.

Visit the workshop page for more details.


BREAKING NEWS: Our Covid-19 virtual tissue model is available for running on nanoHUB!

You can run our model in your browser, without any installations, at nanoHUB (here).

CC3D in nanoHUB project page CC3D in nanoHUB simulation

For more info please visit our CC3D on nanoHUB page.


NEWS: CompuCell3D Multiscale, Virtual-Tissue Spatio-Temporal Modeling of Simulations of COVID-19 Infection, Viral Spread and Immune Response and Treatment Regimes

Simulations of tissue-specific effects of primary acute viral infections like COVID-19 are essential for understanding differences in disease outcomes and optimizing therapeutic interventions. In this two-part mini-workshop we present an open-source Python and CC3DML-scripted multiscale model and simulation of an epithelial tissue infected by a virus, a simplified cellular immune response and viral and immune-induced tissue damage and show how you can use it to model basic patterns of infection dynamics and antiviral treatment. Part I presents the model and teaches how to run it and to change model parameters for generating new biologically meaningful simulations. Part II teaches how to extend the model with additional images, graphics and file outputs, additional cell types, diffusive fields, cell behaviors and interactions and improved subcellular and immune-system models.

For more info and scheduling see here. The Part I and Part II videos are now available on YouTube.


NEW CC3D Version 4.2.2 (July 25, 2020)

We are pleased to announce new version of CompuCell3D. This release includes multiple bug fixes and new features. For more info, and to download the latest version, visit the Downloads page.


We have prepared a YouTube video describing the model described in our preprint.

Covid-19 multicell model on YouTube


Multiscale multicellular modeling of tissue function and disease using CompuCell3D: A simplified computer simulation of acute primary viral infection and immune response in an epithelial tissue

This is a more detailed video presentation hosted by the Pacific Institute for the Mathematical Sciences on the use of CC3D in Covid-19 modeling.
(Click on this image to view the video.)
here here


Call to Contribute: Collaborative Tissue Model Development to Mitigate the Coronavirus Pandemic

attachment:viral_infection_sample_result_1.png

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.

You can run our model online without any installations in https://nanohub.org/tools/cc3dcovid19.

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:

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.


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. This problem should be fixed in CompuCell3d release 4.2.0 (May 2, 2020). If you encounter problems please contact us at <jsluka AT Indiana DOT edu>.


Latest News:

ONLINE CompuCell3D 15th User Training Workshop!

Note: Because of Covid-19, the training workshops will not be held in person. Instead, we will use a combination of teleconferencing (via Zoom), YouTube and other remote access tools. We will keep attendees informed as the details are finalized.

attachment:Workshop20/2020_FINAL_REDonline.pdf

attachment:Workshop20/2020_FINAL_Yellowonline.pdf

attachment:Workshop20/TelleriumFinal.pdf

Combined:

CompuCell3D:

Cellular and Network Modeling:

(click the images to download full size versions of the posters)

July 27th - August 8th, 2020

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 fees.

Facilities: Because of Covid-19, the training workshops will not be held in person. Instead, we will use a combination of teleconferencing (via Zoom), YouTube and other remote access tools. We will keep attendees informed as the details are finalized.

Online Participation: The summer schools will support online participation through Zoom.

Registration: Click here to Register!


CompuCell3D on ...

nanoHUB

CompuCell3D is available for online use on nanoHUB. Some CompuCell3D simulations are already available as demonstrations. See the CC3D on nanoHUB page for more info.


About CompuCell3D

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:

attachment:CC3D1.gif attachment:CC3D2.gif


Support

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.


Try our new CompuCell3D User Forum. In case you are facing any issue with CompuCell3D installation, we are here to help. Please create a post on our subreddit. Problems are often simple to solve.


How to cite CompuCell3D

Multi-Scale Modeling of Tissues Using CompuCell3DM. 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


New Papers using CompuCell3D Simulations have been published:

CompuCell3D: FrontPage (last edited 2020-08-05 20:41:13 by JamesSluka)