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invasion-ruscone

Cancer invasion model from Ruscone et. al

https://github.com/physiboss-models/invasion-ruscone

Science Score: 67.0%

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    Found 7 DOI reference(s) in README
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Repository

Cancer invasion model from Ruscone et. al

Basic Info
  • Host: GitHub
  • Owner: PhysiBoSS-Models
  • Language: C++
  • Default Branch: main
  • Size: 1.46 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created 8 months ago · Last pushed 6 months ago
Metadata Files
Contributing License Code of conduct Citation

https://github.com/PhysiBoSS-Models/Invasion-Ruscone/blob/main/ 

# Invasion-Ruscone DOI

The goal of this model is to study the different modes of cell migration and to predict means to block it by considering not only spatial information obtained from the agent-based simulation but also intracellular regulation obtained from the Boolean model.


## Manuscript

The first version of this model was published in [Multiscale model of the different modes of cancer cell invasion, *Bioinformatics*, June 2023](https://doi.org/10.1093/bioinformatics/btad374). A follow up version was published in the PhysiBoSS tutorial [Building multiscale models with PhysiBoSS, an agent-based modeling tool, *Briefings in Bioinformatics*, November 2024](https://doi.org/10.1093/bib/bbae509).

Owner

  • Name: PhysiBoSS-Models
  • Login: PhysiBoSS-Models
  • Kind: organization

Citation (CITATION.txt) 

If you use PhysiCell in your project, please cite PhysiCell and the version 
number, such as below:                                                      
                                                                             
We implemented and solved the model using PhysiCell (Version 1.14.2) [1].    
                                                                             
[1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
    PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  
    lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018                   
    DOI: 10.1371/journal.pcbi.1005991                                       
                                                                            
Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  
    as below:                                                               
                                                                             
We implemented and solved the model using PhysiCell (Version 1.14.2) [1],    
with BioFVM [2] to solve the transport equations.                           
                                                                             
[1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
    PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  
    lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018                   
    DOI: 10.1371/journal.pcbi.1005991                                       
                                                                             
[2] A Ghaffarizadeh, SH Friedman, and P Macklin, BioFVM: an efficient para- 
    llelized diffusive transport solver for 3-D biological simulations,     
    Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730 
    
If you use PhysiBoSS, please cite as below:

We implemented and solved the model using PhysiCell (Version 1.14.2) [1],    
with PhysiBoSS [2,3] to simulate the intracellular mechanisms.                           

[1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
    PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  
    lar Systems, PLoS Comput. Biol. 14(2): e1005991, 2018                   
    DOI: 10.1371/journal.pcbi.1005991                                       
        
[2] G. Letort, A. Montagud, G. Stoll, R. Heiland, E. Barillot, P. Macklin, 
    A. Zinovyev, and L. Calzone. PhysiBoSS: a multi-scale agent based 
    modelling framework integrating physical dimension and cell signalling. 
    Bioinformatics 35(7):1188-96, 2019. DOI: 10.1093/bioinformatics/bty766.

[3] M. Ponce-de-Leon, A. Montagud, V. Noël, A. Meert, G. Pradas, E. Barillot,
    L. Calzone, and A. Valencia. PhysiBoSS 2.0: a sustainable integration of
    stochastic Boolean and agent-based modelling frameworks. NPJ Systems 
    Biology and Applications 9(1):54, 2023.
    DOI: 10.1038/s41540-023-00314-4 

If you use libRoadrunner, please cite:

    Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias 
    König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro, libRoadRunner: 
    a high performance SBML simulation and analysis library, 
    Bioinformatics 31(20): 3315–21, 2015: DOI: 10.1093/bioinformatics/btv363

If you use PhysiMeSS, please cite: 

    V. Noël, M. Ruscone, R. Shuttle-worth, and C.K. Macnamara. PhysiMeSS--
    A New PhysiCell Addon for Extracellular Matrix Modelling, bioRxiv [preprint] 
    2023.10.27.564365, 2023. DOI: 10.1101/2023.10.27.564365.

GitHub Events

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  • Push event: 13
  • Create event: 10
Last Year
  • Release event: 10
  • Delete event: 7
  • Push event: 13
  • Create event: 10

Dependencies

.github/workflows/build_binaries.yml actions
  • actions/cache v4 composite
  • actions/checkout v4 composite
  • actions/upload-release-asset v1 composite
  • msys2/setup-msys2 v2 composite