Science Score: 18.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
○codemeta.json file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: rheiland
- Language: C++
- Default Branch: main
- Size: 4.66 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
morphy (for ws2022)- you know who you are
Latest:
make -j2
mv morph PhysiCell-model-builder-2.7.3 # want to have the executable in the GUI
cd PhysiCell-model-builder-2.7.3
python bin/pmb.py --studio # or just try to run "studio.sh"
then in the PMB, select the Run tab, press Run Simulation. In Plot tab, Play.
Old/originally:
make -j2
morph
cd output
python cells_info.py 0
python anim_morph.py
Some edits I've made:
* fixed a bug in modules/PhysiCellMultiCellDS.cpp
* "flattened" (filled in all params) of config/PhysiCellsettings.xml (but may have clobbered some of your desired params, e.g., I changed some of the original domain params)
* edited setuptissue() in custom.cpp: for now, just define 4 cells; plus, I think the `axisparams were missing from <user_params>
* addedbeta/animmorph.pyfor simple plotting (and also into /output, but it may get deleted if thecleanor other Makefile target does so)
* cloned/copied the PMB into the root dir (might make it unique to this project)
* hackedphenotypefunctionin custom.cpp to do something silly, but at least provide dynamics, with theaxis_` custom vars
* continue to make tweaks to anim_morph.py
* more to come...
Overnight: * started using the PMB; added ellipse plotting to it * the PMB's /data/morphy.xml is the latest config file * added Didi's tweaks to setuptissue() and new userparams to the .xml * in vis_tab.py, ellipse's angle is a function of the cell's motility vector
Owner
- Name: Randy Heiland
- Login: rheiland
- Kind: user
- Location: Bloomington, IN
- Company: Indiana University
- Website: https://rheiland.github.io/
- Repositories: 210
- Profile: https://github.com/rheiland
Research Associate in @MathCancer Lab. Intelligent Systems Engineering, IU.
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 1.10.4) [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 1.10.4) [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:
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.
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