{"id":49628654,"url":"https://github.com/scientificcomputing/example-paper-fenics","last_synced_at":"2026-05-05T09:06:42.525Z","repository":{"id":63378839,"uuid":"566287442","full_name":"scientificcomputing/example-paper-fenics","owner":"scientificcomputing","description":"Example paper using FEniCS","archived":false,"fork":false,"pushed_at":"2024-05-02T07:40:28.000Z","size":236,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-05T03:42:54.241Z","etag":null,"topics":["fenics","paper"],"latest_commit_sha":null,"homepage":"https://scientificcomputing.github.io/example-paper-fenics/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/scientificcomputing.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-11-15T11:04:12.000Z","updated_at":"2025-01-17T13:34:32.000Z","dependencies_parsed_at":"2023-11-13T11:26:19.612Z","dependency_job_id":"ccf1fb3e-f646-44fd-a629-80db50761d8a","html_url":"https://github.com/scientificcomputing/example-paper-fenics","commit_stats":null,"previous_names":[],"tags_count":10,"template":true,"template_full_name":"scientificcomputing/example-paper","purl":"pkg:github/scientificcomputing/example-paper-fenics","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scientificcomputing%2Fexample-paper-fenics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scientificcomputing%2Fexample-paper-fenics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scientificcomputing%2Fexample-paper-fenics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scientificcomputing%2Fexample-paper-fenics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scientificcomputing","download_url":"https://codeload.github.com/scientificcomputing/example-paper-fenics/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scientificcomputing%2Fexample-paper-fenics/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32642368,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-04T10:08:07.713Z","status":"online","status_checked_at":"2026-05-05T02:00:06.033Z","response_time":54,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["fenics","paper"],"created_at":"2026-05-05T09:06:41.443Z","updated_at":"2026-05-05T09:06:42.517Z","avatar_url":"https://github.com/scientificcomputing.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Supplementary code for the paper: Title of paper\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/scientificcomputing/example-paper-fenics/main?labpath=code%2Fdemo.ipynb)\n\nThis repository contains supplementary code for the paper\n\u003e Finsberg, H., Dokken, J. 2022.\n\u003e Title of paper, Journal of ..., volume, page, url\n\n\n## Abstract\nProvide the abstract of the paper\n\n## Getting started\n\nWe provide a pre-build Docker image which can be used to run the the code in this repository. First thing you need to do is in ensure that you have [docker installed](https://docs.docker.com/get-docker/).\n\nTo start an interactive docker container you can execute the following command\n\n```bash\ndocker run --rm -it ghcr.io/scientificcomputing/example-paper-fenics:latest\n```\n\n## Data\n\nData is available in a dropbox folder. Use the script `download_data.sh` in the data folder to download the data.\n\nThe data folder should have the following structure after the data is downloaded.\n```\n├── README.md\n├── data.tar\n├── download_data.sh\n└── mesh\n    ├── heart01.msh\n    └── heart02.msh\n```\nThese meshes are originally taken from \u003chttps://ora.ox.ac.uk/objects/uuid:951b086c-c4ba-41ef-b967-c2106d87ee06\u003e, but since the original data is about 26GB we decided to make a smaller dataset for this example.\n\nEventually when you publish a paper you could put this data on e.g [Zenodo](https://zenodo.org). That will make sure the data gets it's own DOI.\n\n\n## Scripts\nAll the scripts are located in the folder called `code` in the repository. Is is assumed that you run the script from within this folder.\n\n### Pre-processing\nIn order to reproduce the results you need to first run the pre-processing script\n```\npython3 pre_processing.py\n```\nThis will convert the meshes from Gmsh to a dolfin format.\n\n### Fiber generation\nThe next step is to run the fiber generation. You can do this by running the script\n```\npython3 run_fiber_generation.py\n```\nThis will create a new folder `code/results` containing files called `microstructure_\u003cheart_nr\u003e.h5`.\n\n### Postprocessing\nThe final step is to postprocess the results by running the script\n```\npython3 postprocess.py\n```\nThis will generate a file for visualizing the fibers in the Paraview (inside `code/results` called  `fiber_\u003cheart_nr\u003e.xdmf`). This script will also compare some features computed from the fibers with the results published in the (artificial) paper. If the results differ, then the program will raise an error.\n\n\n\n\n## Citation\n\n```\n@software{Lisa_My_Research_Software_2017,\n  author = {Lisa, Mona and Bot, Hew},\n  doi = {10.5281/zenodo.1234},\n  month = {12},\n  title = {{My Research Software}},\n  url = {https://github.com/scientificcomputing/example-paper},\n  version = {2.0.4},\n  year = {2017}\n}\n```\n\n\n## Having issues\nIf you have any troubles please file and issue in the GitHub repository.\n\n## License\nMIT\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscientificcomputing%2Fexample-paper-fenics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscientificcomputing%2Fexample-paper-fenics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscientificcomputing%2Fexample-paper-fenics/lists"}