{"id":21312530,"url":"https://github.com/phydev/angio","last_synced_at":"2026-01-02T09:21:16.924Z","repository":{"id":151473206,"uuid":"44310125","full_name":"phydev/angio","owner":"phydev","description":"Developing a 3D phase-field modelling for tumor angiogenesis","archived":false,"fork":false,"pushed_at":"2024-04-16T19:34:23.000Z","size":1695,"stargazers_count":1,"open_issues_count":0,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-22T10:11:30.079Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://phydev.github.io/angio","language":"Fortran","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/phydev.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-10-15T10:18:34.000Z","updated_at":"2024-10-06T16:15:24.000Z","dependencies_parsed_at":"2024-04-16T20:54:31.732Z","dependency_job_id":null,"html_url":"https://github.com/phydev/angio","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/phydev%2Fangio","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/phydev%2Fangio/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/phydev%2Fangio/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/phydev%2Fangio/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/phydev","download_url":"https://codeload.github.com/phydev/angio/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243790949,"owners_count":20348379,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-21T17:34:12.583Z","updated_at":"2026-01-02T09:21:16.898Z","avatar_url":"https://github.com/phydev.png","language":"Fortran","funding_links":[],"categories":[],"sub_categories":[],"readme":"![build status](https://github.com/phydev/angio/actions/workflows/docker-image.yml/badge.svg)\n\n----\n\n## Angiogenesis Project\n\nThis project is hosted by the [CFisUC](http://cfisuc.fis.uc.pt/) at the [University of Coimbra](www.uc.pt) \nand consists in a phase-field model for tumor angiogenesis. The model is based on the paper published by\n[Travasso et al. (2011)](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019989) with some physical and computational improvements.\n\n###  What is new on v6.0.s\n\n- Coupled the blood flow and the hypoxic cell deactivation;\n- The hypoxic cells have volume;\n- The system is modeled in three dimensions;\n- tools: Routines to measure the number of branches, anastomoses and the vessels diameter;\n\n### Running with Docker\n\n1. Build the image:\n```docker build --platform linux/x86_64 -t angio docker/``` (the ```--platform``` flag is necessary for the image to run on Apple Silicon)\n2. Run the container:\n```docker run -it -v $(pwd):/code angio /bin/bash run.sh \u003crun_id\u003e```. Please make sure that an input file named ```inp\u003crun_id\u003e``` is present in the root directory of the project.\n\n### Parameters\n\nWe provide typical parameters for simulations in [`input_file`](https://github.com/phydev/angio/blob/master/input_file). \nSee 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).\n\n\n| Reference value | Variable               | Description                            |\n|-----------------|-----------------------|----------------------------------------|\n| 4.00 | cell_radius | Radius of individual cells |\n| 100.0 | diffusion_const | Diffusion constant for VEGF |\n| 1.00 | interface_width | Width of the phase-field interface |\n| 0.30 | vegf_p | VEGF concentration for maximum proliferation |\n| 0.09 | vegf_c | VEGF concentration for branching |\n| 20.0 | diff_oxy_length | Diffusion length for oxygen |\n| 6.25 | vegf_rate | Rate of VEGF uptake by cells |\n| 1.00 | vegf_source_conc | Concentration of VEGF at source |\n| 1.00 | prolif_rate | Rate of proliferation of endothelial cells |\n| 5.00 | vessel_radius | Initial radius of blood vessels |\n| 150000 | total_time_step | Total time steps for simulation |\n| 0.0010 | dt | Time step size |\n| 800.00 | chi_chemiotactic_resp | Chemotactic response of endothelial cells |\n| 100, 100, 50,  1, 1, 1 | Lx_Ly_Lz_dx_dy_dz | Simulation domain size and grid spacing |\n| -754333222 | random_seed | Seed for random number generation - must be negative |\n| 20 | number_of_boundary_points | Number of boundary points to keep track |\n| 10000 | source_max | Maximum number of VEGF source points |\n| 0.01 | vegf_grad_min | Threshold for VEGF gradient |\n| 0.03 | vegf_max | Maximum VEGF concentration |\n| 2.00 | depletion_weight | Energy cost to avoid overlap between vessels and hypoxic cells |\n| 2000 | output_period | Time period between outputting results |\n| 40000 | extra_steps | Additional time steps for simulation |\n| 4000 | max_number_of_tip_cells | Maximum number of tip cells allowed |\n| T | thinning_FT | Flag for using thinning algorithm |\n| F | periodic_FT | Flag for using periodic boundary conditions |\n| F | flow_FT | Flag for computing the blood flow |\n\n\n\nBeware 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. \n\n### Postprocessing tools\n\nIn 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).\n\n### Publications\n\nM. Moreira-Soares, R. Coimbra, L. Rebelo, J. Carvalho \u0026 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)\n\n\n![alt tag](https://moreirasm.files.wordpress.com/2018/06/300ms.gif?w=364\u0026h=335)\n\n### Acknowledgements\n\nSpecial thanks to [João Simões](https://github.com/joaoplay) for supporting the long term reproducibility of this code by dockerizing the repository. \n\nThis project was funded by the National Council of Technological and Scientific Development (CNPq - Brazil) under the grant 235101/2014-1. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fphydev%2Fangio","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fphydev%2Fangio","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fphydev%2Fangio/lists"}