https://github.com/phydev/angio
Developing a 3D phase-field modelling for tumor angiogenesis
https://github.com/phydev/angio
Last synced: 5 months ago
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Developing a 3D phase-field modelling for tumor angiogenesis
- Host: GitHub
- URL: https://github.com/phydev/angio
- Owner: phydev
- License: gpl-2.0
- Created: 2015-10-15T10:18:34.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2024-04-16T19:34:23.000Z (about 2 years ago)
- Last Synced: 2025-01-22T10:11:30.079Z (over 1 year ago)
- Language: Fortran
- Homepage: http://phydev.github.io/angio
- Size: 1.62 MB
- Stars: 1
- Watchers: 2
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
----
## Angiogenesis Project
This project is hosted by the [CFisUC](http://cfisuc.fis.uc.pt/) at the [University of Coimbra](www.uc.pt)
and consists in a phase-field model for tumor angiogenesis. The model is based on the paper published by
[Travasso et al. (2011)](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019989) with some physical and computational improvements.
### What is new on v6.0.s
- Coupled the blood flow and the hypoxic cell deactivation;
- The hypoxic cells have volume;
- The system is modeled in three dimensions;
- tools: Routines to measure the number of branches, anastomoses and the vessels diameter;
### Running with Docker
1. Build the image:
```docker build --platform linux/x86_64 -t angio docker/``` (the ```--platform``` flag is necessary for the image to run on Apple Silicon)
2. Run the container:
```docker run -it -v $(pwd):/code angio /bin/bash run.sh ```. Please make sure that an input file named ```inp``` is present in the root directory of the project.
### Parameters
We provide typical parameters for simulations in [`input_file`](https://github.com/phydev/angio/blob/master/input_file).
See the description of each paramter in the table bellow and the mapping with experimental data in [Supplementary material](https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-018-27034-8/MediaObjects/41598_2018_27034_MOESM1_ESM.pdf).
| Reference value | Variable | Description |
|-----------------|-----------------------|----------------------------------------|
| 4.00 | cell_radius | Radius of individual cells |
| 100.0 | diffusion_const | Diffusion constant for VEGF |
| 1.00 | interface_width | Width of the phase-field interface |
| 0.30 | vegf_p | VEGF concentration for maximum proliferation |
| 0.09 | vegf_c | VEGF concentration for branching |
| 20.0 | diff_oxy_length | Diffusion length for oxygen |
| 6.25 | vegf_rate | Rate of VEGF uptake by cells |
| 1.00 | vegf_source_conc | Concentration of VEGF at source |
| 1.00 | prolif_rate | Rate of proliferation of endothelial cells |
| 5.00 | vessel_radius | Initial radius of blood vessels |
| 150000 | total_time_step | Total time steps for simulation |
| 0.0010 | dt | Time step size |
| 800.00 | chi_chemiotactic_resp | Chemotactic response of endothelial cells |
| 100, 100, 50, 1, 1, 1 | Lx_Ly_Lz_dx_dy_dz | Simulation domain size and grid spacing |
| -754333222 | random_seed | Seed for random number generation - must be negative |
| 20 | number_of_boundary_points | Number of boundary points to keep track |
| 10000 | source_max | Maximum number of VEGF source points |
| 0.01 | vegf_grad_min | Threshold for VEGF gradient |
| 0.03 | vegf_max | Maximum VEGF concentration |
| 2.00 | depletion_weight | Energy cost to avoid overlap between vessels and hypoxic cells |
| 2000 | output_period | Time period between outputting results |
| 40000 | extra_steps | Additional time steps for simulation |
| 4000 | max_number_of_tip_cells | Maximum number of tip cells allowed |
| T | thinning_FT | Flag for using thinning algorithm |
| F | periodic_FT | Flag for using periodic boundary conditions |
| F | flow_FT | Flag for computing the blood flow |
Beware that the input file `inp001` is solely used to run the docker image with Github actions. The parameters were changed to produce a short simulation with small grid, few iterations, and no sources of VEGF. Please do __not__ base future studies on this file.
### Postprocessing tools
In the folder `tools` we have scripts to postprocess the data generated with the simulations. The documentation for each script is found [here](https://github.com/phydev/angio/blob/master/tools/about.md).
### Publications
M. Moreira-Soares, R. Coimbra, L. Rebelo, J. Carvalho & R. D. M. Travasso. [Angiogenic Factors produced by Hypoxic Cells are a leading driver of Anastomoses in Sprouting Angiogenesis–a computational study](https://www.nature.com/articles/s41598-018-27034-8). Scientific Reports 8, 8726 (2018)
### Acknowledgements
Special thanks to [João Simões](https://github.com/joaoplay) for supporting the long term reproducibility of this code by dockerizing the repository.
This project was funded by the National Council of Technological and Scientific Development (CNPq - Brazil) under the grant 235101/2014-1.