Description

The Engineered nanoBIO node at Indiana University (IU) develops a powerful set of integrated computational nanotechnology products that address this complex, multiscale problem in both education and research and facilitate the discovery of customized, efficient, and safe nanoscale devices for biological applications. These apps, tools, and frameworks span the range from nanoscale particles (nano) to cellular scale structures (micro) to tissue scale morpohologies (macro).

Tools (1-20 of 47)

1. Cycle Training App for PhysiCell

   Tools | 18 Dec 2020 | Contributor(s):: Furkan Kurtoglu, Aneequa Sundus, Kali Nicole Konstantinopoulos, Drew Willis, Mary Chen, Randy Heiland, Paul Macklin

   Training application for "Cycle" concept in PhysiCell.

2. PhysiCell model for tumor hypoxia

   Tools | 07 Aug 2020 | Contributor(s):: Lima Da Rocha, Heber, Paul Macklin, Furkan Kurtoglu

   Multicellular simulation in 2-D of tumor hypoxia.

3. COVID-19 data analysis

   Tools | 07 Aug 2020 | Contributor(s):: Randy Heiland, Paul Macklin

   Perform data analysis in a Jupyter notebook using data from the pc4covid19 tool.

4. Multicellular modeling of SARS-CoV-2 dynamics and virion mediated cell fusion with antiviral drug effects

   Tools | 27 Jul 2020 | Contributor(s):: Yafei Wang, Michael Getz, Randy Heiland, Paul Macklin

   Simulate SARS-CoV-2 dynamics and virion mediated cell fusion under pharmacodynamics effects with PhysiCell

5. CompuCell3D v4 Main Tool

   Tools | 08 Jun 2020 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

   Base tool for CompuCell3D version 4 and greater. Allows running any of the demos included with CC3D (/CompuCell3D_Demos/Demos)

6. CompuCell3D - 2D wet foam coarsening

   Tools | 04 Jun 2020

   Simulates foam coarsening in a 2D wet foam

7. CompuCell3D - 2D wet foam coarsening with drainage

   Tools | 04 Jun 2020

   Simulation of 2D wet foam with drainage (gravity)

8. CompuCell3D - Cells random walking at different speeds

   Tools | 04 Jun 2020 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

   Cells random walking at different speeds implemented through the motility plugin

9. CompuCell3d cell sorting in a hexagonal lattice

   Tools | 04 Jun 2020 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

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

10. CompuCell3D - Delta-Notch signaling in a group of cells

    Tools | 04 Jun 2020 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

    CompuCell3D can solve individual cell's ODE and have the information of one cell affect another (implemented trough SBML)

11. CompuCell3D v4 - Bacterium Macrophage simulation

    Tools | 04 Jun 2020 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

    Macrophage hunts bacterium in a maze

12. CompuCell3D - Simulation of angiogenesis

    Tools | 04 Jun 2020 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

    CompuCell3D simulates angiogenesis using chemical signals

13. COVID 19 Virtual Tissue Model - Tissue Infection and Immune Response Dynamics

    Tools | 26 May 2020 | Contributor(s):: T.J. Sego, Josua Oscar Aponte-Serrano, Juliano Ferrari Gianlupi

    Simulates tissue and immune system interactions during a viral lung infection

14. A virion infected-cell response tissue simulator

    Tools | 13 Apr 2020 | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin

    Simulate infected cell response to virus with PhysiCell

15. A virion replication tissue simulator

    Tools | 13 Apr 2020 | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin

    Simulate virus replication dynamics with PhysiCell

16. A virion endocytosis tissue simulator

    Tools | 13 Apr 2020 | Contributor(s):: Yafei Wang, Randy Heiland, Paul Macklin

    Simulate virus endocytosis (internalization), ACE2 receptor dynamics with PhysiCell

17. Souffle: Virus Capsid Assembly Lab

    Tools | 01 Apr 2020 | Contributor(s):: Nilsson, Lauren, JCS Kadupitiya, Vikram Jadhao

    Simulate assembly of flexible capsomeres into virus capsids and oligomers

18. PhysiCell model for COVID19

    Tools | 26 Mar 2020 | Contributor(s):: Randy Heiland, Yafei Wang, Paul Macklin

    Prototype 2-D multicellular simulation of COVID19.

19. Mechanics Training App for PhysiCell

    Tools | 14 Feb 2020 | Contributor(s):: Furkan Kurtoglu, Aneequa Sundus, Mishler, Daniel S, Randy Heiland, Paul Macklin

    Training application for "Mechanics" concept in PhysiCell.

20. PhysiCell model with SBML intracellular model

    Tools | 10 Feb 2020 | Contributor(s):: Randy Heiland

    Each cell will have its own intracellular (metabolic) model that will affect the microenvironment.