Cancer

COVID-19

General Multicellular Systems

Basic Biophysics and Training

Externally Developed Apps

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Soft-matter-based Nanoscale Systems

Ionic Self Assembly

Ions in Nanoconfinement (nano)

This app empowers users to simulate ions confined between material surfaces that are nanometers apart, and extract the associated ionic structure. The app facilitates investigations for a wide array of ionic and environmental parameters using standard molecular dynamics (MD) method for unpolarizable surfaces.

• Launch the app
• Documentation

Nanosphere Electrostatics Lab (nano)

This app allows users to simulate the self-assembly of ions near a spherically shaped nanoparticle, and extract the effective electrostatic properties..

• Launch the app

Nanoparticle Self Assembly

Nanoparticle Assembly Lab (nano)

Simulate assembly of nanoparticles into aggregates in physiological conditions.

 

Polyvalent Nanoparticle Binding Simulator (nano)

Simulates the binding of ligand-decorated nanoparticles to cell membrane driven by ligand-cell-receptor attraction

 

Souffle: Virus Capsid Assembly Lab (nano)

Simulate assembly of flexible capsomeres into virus capsids and oligomers.

 

Nanoparticle Shape Lab  (nano)

The shape of nanocontainers determines their ability to act as targeted drug delivery carriers by modulating their biodistribution and bioavailability.  This app simulates the shape deformation of soft-matter-based deformable, charged nanocontainers for a broad variety of nanocontainer material properties and solution conditions. Molecular dynamics based simulated annealing is used to minimize the energy of the nanocontainer for a given set of material and solution parameters.

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Cancer apps

Compucell3D Vascular Tumor (micro)

Simulate 3D vascular tumor with CompuCell3D

 

PhysiCell: cancer nanotherapy simulator (macro)

This app allows users to design and explore new and novel nanotherapies, where engineered nanoparticles are conjugated to novel cancer therapeutics. Users can simulate the growth and migration of cancer cells in the tissue environment, as well as pharamcodynamic response to user-designed therapeutics. Adapted from the PhysiCell Framework

  PhysiCell: cancer biorobots simulation (macro)

  2D simulation of biorobots delivering a drug to cancer cells

 

PhysiCell: cancer-immune model (macro)

  PhysiCell model of immune cells attacking a heterogeneous tumor

 

PhysiCell: tumor heterogeneity (macro)

  2D simulation of tumor heterogeneity

 

PhysiCell: liver tissue mechanobiology (macro)

Simulates the liver tissue mechanobiology on cancer metastatic seeding.

 

PhysiCell: AMIGOS - Hypoxia (macro)

Hypoxic conditions occur in the center of tumor after tumor cells use and deplete oxygen. Hypoxic cells secrete signaling chemicals to induce vascularization, such as vascular epithelial growth factor (VEGF).

 

CompuCell3D - Simulation of Angiogenesis

In this tool we simulate a bacterium secreting a diffusive chemical signal, the macrophage is able to detect the gradient of this signal and thus hunt the macrophase. In CompuCell3D the default view is of the cells, we can change the view to observe the chemical field by selecting the drop-down menu in the "Graphics 0" window and selecting it (in the case of this tool the chemical is named ATTR). If you don't see the cells anymore when changing to this view make sure that cell borders is selected under Visualizations option menu.

PhysiCell Model for Tumor Hypoxia

This app demonstrates the evaluation of the new hypotheses on the frequency and duration of phenotypic changes in cancer cells under the influence of hypoxic conditions.

This model and cloud-hosted demo are part of a collaboration between Dr. Macklin's lab and Dr. Gilkes's lab, through of a project granted by Jayne Koskinas Ted Giovanis (JKTG) Foundation for Health and Policy and the Breast Cancer Research Foundation (BCRF). It is also part of the education and outreach for the IU Engineered nanoBIO Node and the NCI-funded cancer systems biology grant U01CA232137. The model is built using PhysiCell: a C++ framework for multicellular systems biology [1].

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COVID-19 apps

COVID 19 Virtual Tissue Model - Tissue Infection and Immune Response Dynamics (micro)

Simulates tissue and immune system interactions during a viral lung infection

 

PhysiCell for COVID-19 (macro)

  This model simulates replication dynamics of SARS-CoV-2 (coronavirus / COVID19) in a layer of epithelium. It is being rapidly prototyped and refined with community support. See related: PC4COVID19: Rapid Community Prototyping of a Coronavirus (COVID-19) Replication Simulator

COVID-19 Data Analysis Educational Tool

This educational tool provides users with a Jupyter notebook that teaches them how to use Python to analyze and visualize some pre-computed data from the https://nanohub.org/tools/pc4covid19 app. Because it is an interactive notebook, users can edit the Python code and explore on their own.

PhysiCell: Infected System and Off-Site Immune System

In this App, we developed a dynamic interaction model which contains two systems: an infected system of cells and a off-site immune system that respond to the infection. We observe that immune response changes depending on the intensity of the infection cells. Our aim is to investigate how the immune system modulate its response according to variation in the infection.

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General Multicellular Systems

CompuCellSort (micro)

simulate cell sorting with compucell 3d

 

PhysiCell: Thanos vs. Avengers multicellular demonstrator (macro)

This app demonstrates chemotactic migration, cell-cell contact interactions, and iterating across cells to apply a random event. It also explores the impact of varying the number and strength of different cells in a complex, stochastic adversarial system.

CompuCell3D v4 Main Tool

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 intuitive and make Virtual Tissue modeling accessible to users without extensive software development or programming experience. It uses Cellular Potts Model to model cell behavior.

CompuCell3D v3

An open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. Uses Cellular Potts Model to model cell behavior. This version is still supported for models that are specifically developed for this version.

CompuCell3D 3D Cell Sorting

CompuCell3D based application to simulate 3D cell sorting

CompuCell3d cell sorting in a hexagonal lattice

Showcases hexagonal lattice use in CompuCell3D by simulating cell sorting by difference in contact energies in a hexagonal lattice.

CompuCell3D - 2D wet foam coarsening

CompuCell3D Demo for a 2D foam coarsening without drainage (gravity). This simulations seeds space with cells representing air bubbles, they are allowed to relax to their target volume with no other cell type present. On time step 200 the simulation's empty space is filled with cells representing water. The whole system is allowed to relax for another 100 time steps then air bubbles have their volume constrain removed, i.e. can freely change their volumes.

CompuCell3D - 2D wet foam coarsening with drainage

CompuCell3D Demo for a 2D foam coarsening with drainage (gravity). This simulations seeds space with cells representing air bubbles, they are allowed to relax to their target volume with no other cell type present. On time step 200 the simulation's empty space is filled with cells representing water. The whole system is allowed to relax for another 100 time steps then air bubbles have their volume constrain removed, i.e. can freely change their volumes. On time step 500 gravity (drainage) is turned on and water cells accumulate at the bottom of the simulation.

CompuCell3D - Delta-Notch signaling in a group of cells

CompuCell3D can solve individual cell's ODE and have the information of one cell affect another (implemented trough SBML). Cells participating in Delta-Notch signaling. You can visualize Delta and Notch levels field by selecting the drop-down menu in the "Graphics" window and selecting one of them (changing the chemical visualized pauses the simulation, you'll need to hit run after the change). You can have more than one "Graphics" window open by selecting the menu "Visualization->New Graphics Window"

PhysiCell biorobots simulation 

2D simulation of director, worker, and cargo cells.

Three-Type Multicellular Simulation Lab

Inspired by the 3-body problem in physics, this virtual cell laboratory explores a tunable multicellular system with 3 interacting cell types. Similarly to the 3-body problem, simple cell-cell interactions can lead to complex emergent dynamics, including cooperativity, competition, oscillations, and chaotic phenomena.

This virtual cell lab lets you broadly explore the effects of your assumptions of how cells affect one another to drive the emergent multicelular dynamics.

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Basic Biophysics and Training

Compucell3D Bacterium Macrophage (micro)

Simulation of macrophage chasing bacterium

 

PhysiCell: biased random migration generator (macro)

  PhysiCell demonstration of biased random cell migration

 

PhysiCell: Motility Training App (macro)

To account for cell movement, PhysiCell includes a set of parameters that govern speed and direction of cell motility. The biased, random motility of cells is determined by the following equation:where b is the level of bias in movement (migration bias), ξ is a random unit vector of length 1, and dbias is the direction.

PhysiCell: invader-scout-attacker system (macro)

  PhysiCell model of an invader-scout-attacker multicellular system

 

PhysiCell workshop training (macro)

This tool is intended to be used at PhysiCell training workshops. It is general purpose in the sense that it provides a GUI that includes 1) a Terminal tab to compile and run a PhysiCell model, and 2) a Plotting tab to visualize results.

Volume Training App for PhysiCell 

Training application for "Volume" concept in PhysiCell.

Motility Training App 

Training application for "Motility" concept in PhysiCell. To account for cell movement, PhysiCell includes a set of parameters that govern speed and direction of cell motility. The biased, random motility of cells is determined by the following equation:

where b is the level of bias in movement (migration bias), ξ is a random unit vector of length 1, and d_bias is the direction of the bias.

Death Training App for PhysiCell  

Training application for "Death" concept in PhysiCell. Cells do not keep growing and dividing forever. Eventually, they undergo cell death, in which cells lyse (burst) and decay. PhysiCell supports two models of cell death: apoptosis and necrosis. Apoptosis is programmed cell death, which contributes to regular growth and function. Necrosis, on the other hand, is unprogrammed cell death due to injury or disease. PhysiCell users may choose the model(s) appropriate for their projects.

Microenvironment Concept Training App for PhysiCell 

Training application for "Microenvironment" concept in PhysiCell.

Mechanics Training App for PhysiCell 

Training application for "Mechanics" concept in PhysiCell.

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Externally Developed Apps