New Seminars available on Multiscale Modeling with Compucell3D

30 Years!

Our Collaboratory Projects

We collaborate extensively with several other computational biology tools groups. In particular:

Tissue Forge

Tissue Forge is a continuation of the Mechanica project. The goal of Tissue Forge is to deliver a modeling and simulation framework that lets users from all relevant backgrounds interactively create, simulate and explore models at biologically relevant length scales. We believe that accessible and interactive modeling and simulation is key to increasing scientific productivity, much like how modeling environments have revolutionized many fields of modern engineering.

Mechanica

The invitation to join the IMAG/MSM working group is here.

NEWS: We have viral infection model papers!

"A Multiscale Multicellular Spatiotemporal Model of Local Influenza Infection and Immune Response", Sego, T. J., Mochan, E. D., Ermentrout, G. B., & Glazier, J. A. (2021). Journal of theoretical biology, 532, 110918. Full Text

"Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2", Ferrari Gianlupi J, Mapder T, Sego TJ, Sluka JP, Quinney SK, Craig M, Stratford RE Jr, Glazier JA. Viruses. 2022 Mar 14;14(3):605. doi: 10.3390/v14030605. PMID: 35337012; PMCID: PMC8953050. Full Text

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 (here).

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.

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

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.)

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.

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:

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

National Institute of Health, National Institute of Biomedical Imaging and Bioengineering (NIBIB) Grant U24EB028887, "Dissemination of libRoadRunner and CompuCell3D".

Past support for this project includes:

U.S. 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

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.

How to cite CompuCell3D

For a more complete list see our Publication Page.

• Mathematical and In Silico Analysis of Synthetic Inhibitory Circuits That Program Self-Organizing Multicellular Structures

• Design and mathematical analysis of activating transcriptional amplifiers that enable modular temporal control in synthetic juxtacrine circuits, Synthetic and Systems Biotechnology

• A Multiscale Spatial Modeling Framework for the Germinal Center Response.

• Morphological basis of the lung adenocarcinoma subtypes

• Programming Juxtacrine-Based Synthetic Signaling Networks in a Cellular Potts Framework

• A Cellular Potts Model of the interplay of synchronization and aggregation

• Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2

• Shape-velocity correlation defines polarization in migrating cell simulations

• CompuCell3D simulations reproduce mesenchymal cell migration on flat substrates.

• Fibroblast state switching orchestrates dermal maturation and wound healing

• Computational Model of Secondary Palate Fusion and Disruption

• Multi-scale modeling of the CD8 immune response.

• Virtual-Tissue Computer Simulations Define the Roles of Cell Adhesion and Proliferation in the Onset of Kidney Cystic Disease

• IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8+ T cell-APC: a multiscale modeling study.

• Spheroid Formation of Hepatocarcinoma Cells in Microwells: Experiments and Monte Carlo Simulations

• A Computational Model of Peripheral Photocoagulation for the Prevention of Progressive Diabetic Capillary Occlusion

• A Liver-Centric Multiscale Modeling Framework for Xenobiotics

• Somites Without a Clock

• Dynamics of cell aggregates fusion: Experiments and simulations

• Synergy of cell–cell repulsion and vacuolation in a computational model of lumen formation

• The effects of cell compressibility, motility and contact inhibition on the growth of tumor cell clusters using the Cellular Potts Model

• Advances in Modelling of Epithelial to Mesenchymal Transition

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