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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
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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.
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Cancer Evolution in CompuCell3D
27 May 2021 | Contributor(s):: Juliano Ferrari Gianlupi, James A Glazier
Demonstrates implemetation of cancer evolution in CompuCell3D
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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.
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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.
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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)
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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.
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PhysiCell 3D tumor
20 Jan 2021 | | Contributor(s):: Randy Heiland, Paul Macklin, Koudoro, Serge, Javier Guaje
Simulate a 3D spheroid cancer tumor with PhysiCell
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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.
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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.
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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
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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
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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.
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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.
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Molecular Spectroscopy
12 Aug 2020 | | Contributor(s):: Michael Earl Reppert
Front-end for content of Purdue course CHM676 (Molecular Spectroscopy).
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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.
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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.
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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
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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)
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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