physicell_gpu
Science Score: 54.0%
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
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 1 committers (100.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.4%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: matt-stack
- License: mit
- Language: C++
- Default Branch: main
- Size: 4.13 MB
Statistics
- Stars: 5
- Watchers: 2
- Forks: 1
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
PhysiCell_GPU: an OpenACC Acclerated Version of PhysiCell, an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems.
In this code, we carefully utilize OpenACC, adirective-based programming model to accelerate the diffusion portion in Equation 1 inPhysiCell, a cross-platform agent-based biosimulationframework that has been adopted in cancer infectious diseases and othercomplex biological problem.
Compile uses NVHPC, but you can change it in the Makefile. To build, just type make. The default is using Cuda managed memory.
Original: https://github.com/MathCancer/PhysiCell
Reference: A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellular Systems, PLoS Comput. Biol. 14(2): e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991
Visit http://MathCancer.org/blog for the latest tutorials and help.
Owner
- Name: Matt Stack
- Login: matt-stack
- Kind: user
- Location: California
- Company: NVIDIA
- Repositories: 32
- Profile: https://github.com/matt-stack
Solution Architect at NVIDIA
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 1.6.0) [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 1.6.0) [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
GitHub Events
Total
- Issues event: 1
- Issue comment event: 1
Last Year
- Issues event: 1
- Issue comment event: 1
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Matt Stack | m****t@u****u | 4 |
Committer Domains (Top 20 + Academic)
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Last synced: 7 months ago
All Time
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- Total pull requests: 0
- Average time to close issues: N/A
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- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
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- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
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- Bot issues: 0
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Top Authors
Issue Authors
- Rodolfo-Gallegos (1)