Tools (1-20 of 149)

1. CompuCell3D - Simulation of cell crawling in 3D

   03 Feb 2022

   Deploys the CompuCell3D simulation of cell crawling in 3D by Fortuna et al. 2020 https://doi.org/10.1016/j.bpj.2020.04.024

2. Tuberculosis Model Incorporating Treatment, Vaccination, and Antibiotic Resistance

   27 May 2021 | Contributor(s):: Antonio Zdanis Neher

   Run though an interactive application to learn more about the consequences of antibiotic resistant pathogens through the lens of Tuberculosis.

3. Cancer Evolution in CompuCell3D

   27 May 2021 | Contributor(s):: Juliano Ferrari Gianlupi, James A Glazier

   Demonstrates implemetation of cancer evolution in CompuCell3D

4. FocalPointPlasticity Plugin Demo

   19 May 2021 | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

   This simple demo shows basic functionality of FocalPointPlasticity and how link rigidity affects cell behaviors.

5. CompuCell3D - Chemotactic Elongation Demo

   30 Mar 2021 | | Contributor(s):: Juliano Ferrari Gianlupi, T.J. Sego

   Implementation of Developmental biology 289.1 (2006): 44-54. and PLoS Comput Biol 4.9 (2008): e1000163.

6. PhysiCell simulation of GBM tumour under oHSV1 treatment

   28 Mar 2021 | | Contributor(s):: Adrianne Jenner, Randy Heiland, Paul Macklin

   Simulation for GBM fragment growth under oHSV1 treatment published in Jenner et al. (2021)

7. A Vaccine Model for COVID-19

   25 Jan 2021 | | Contributor(s):: Kali Nicole Konstantinopoulos, James A Glazier (editor), Josua Oscar Aponte-Serrano (editor)

   Simulate the introduction of a vaccine in the COVID-19 pandemic, focused on the US.

8. PhysiCell 3D tumor

   20 Jan 2021 | | Contributor(s):: Randy Heiland, Paul Macklin, Koudoro, Serge, Javier Guaje

   Simulate a 3D spheroid cancer tumor with PhysiCell

9. Influenza In Host Kinetics Model

   19 Dec 2020 | | Contributor(s):: Hanna, Tyler Scott, James A Glazier, Josua Oscar Aponte-Serrano

   Module explaining the in-host viral kinetics of IAV under different conditions.

10. Cycle Training App for PhysiCell

    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.

11. Three-Type Multicellular Simulation Lab

    09 Nov 2020 | | Contributor(s):: Paul Macklin, Randy Heiland

    An analog of the 3-body problem: modeling 3 interacting cell types in a dynamic environment

12. PhysiBoSS simulation of COVID19 infection

    27 Oct 2020 | | Contributor(s):: Vincent Noel, Miguel Ponce de Leon, Anna Niarakis, Laurence Calzone, Alfonso Valencia, Arnau Montagud

    PhysiBoSS-COVID: the Boolean modelling of COVID-19 signalling pathways in a multicellular simulation framework

13. Photosynthetic Protein Spectroscopy Lab

    19 Oct 2020 | | Contributor(s):: Safa Ahad, Chientzu Lin, Michael Earl Reppert

    This tool parses PDB structures of photosynthetic proteins to identify pigments, calculate inter-pigment interactions, and simulate optical spectra for the complex.

14. Amide I Vibrational Spectroscopy Lab

    24 Sep 2020 | | Contributor(s):: Michael Earl Reppert, Jacob Hnatusko Wat

    This tool allows users to upload/fetch protein databank files, visualize the protein structure, and calculate Amide I vibrational spectra for the protein.

15. Molecular Spectroscopy

    12 Aug 2020 | | Contributor(s):: Michael Earl Reppert

    Front-end for content of Purdue course CHM676 (Molecular Spectroscopy).

16. PhysiCell model for tumor hypoxia

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

    Multicellular simulation in 2-D of tumor hypoxia.

17. COVID-19 data analysis

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

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

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

    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

19. CompuCell3D v4 Main Tool

    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)

20. CompuCell3D - Cells random walking at different speeds

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

    Cells random walking at different speeds implemented through the motility plugin