{"id":18658694,"url":"https://github.com/mcellteam/mcell","last_synced_at":"2025-10-11T21:39:46.807Z","repository":{"id":8612641,"uuid":"10253341","full_name":"mcellteam/mcell","owner":"mcellteam","description":"MCell Monte Carlo Simulator of Cellular Microphysiology","archived":false,"fork":false,"pushed_at":"2025-05-02T20:24:43.000Z","size":89527,"stargazers_count":35,"open_issues_count":14,"forks_count":11,"subscribers_count":21,"default_branch":"master","last_synced_at":"2025-08-24T20:37:08.879Z","etag":null,"topics":["cellblender","mcell","simulation"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mcellteam.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.txt","contributing":null,"funding":null,"license":"LICENSE.txt","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,"zenodo":null}},"created_at":"2013-05-23T20:59:54.000Z","updated_at":"2025-05-02T17:04:57.000Z","dependencies_parsed_at":"2025-04-11T21:41:51.885Z","dependency_job_id":"b8e18960-4072-44c1-8500-697f5596fb77","html_url":"https://github.com/mcellteam/mcell","commit_stats":{"total_commits":4478,"total_committers":44,"mean_commits":"101.77272727272727","dds":0.6042876284055382,"last_synced_commit":"3920aec22c55013b78f7d6483b81f70a0d564d22"},"previous_names":[],"tags_count":28,"template":false,"template_full_name":null,"purl":"pkg:github/mcellteam/mcell","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mcellteam","download_url":"https://codeload.github.com/mcellteam/mcell/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mcellteam%2Fmcell/sbom","scorecard":{"id":631895,"data":{"date":"2025-08-11","repo":{"name":"github.com/mcellteam/mcell","commit":"80ca633fbc00ebc1867f2873e17337562d5100f7"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":3.1,"checks":[{"name":"Code-Review","score":0,"reason":"Found 0/30 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Dangerous-Workflow","score":-1,"reason":"no workflows found","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Token-Permissions","score":-1,"reason":"No tokens found","details":null,"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"SAST","score":0,"reason":"no SAST tool detected","details":["Warn: no pull requests merged into dev branch"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"License","score":9,"reason":"license file detected","details":["Info: project has a license file: LICENSE.txt:0","Warn: project license file does not contain an FSF or OSI license."],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":-1,"reason":"internal error: error during branchesHandler.setup: internal error: githubv4.Query: Resource not accessible by integration","details":null,"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Fuzzing","score":10,"reason":"project is fuzzed","details":["Info: CppLibFuzzer integration found: libs/jsoncpp/src/test_lib_json/fuzz.cpp:18","Info: CppLibFuzzer integration found: libs/jsoncpp/src/test_lib_json/main.cpp:3746"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: pipCommand not pinned by hash: libs/jsoncpp/.travis_scripts/travis.install.linux.sh:6","Info:   0 out of   1 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Vulnerabilities","score":3,"reason":"7 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2018-34 / GHSA-2fc2-6r4j-p65h","Warn: Project is vulnerable to: PYSEC-2021-856 / GHSA-5545-2q6w-2gh6","Warn: Project is vulnerable to: PYSEC-2019-108 / GHSA-9fq2-x9r6-wfmf","Warn: Project is vulnerable to: PYSEC-2018-33 / GHSA-cw6w-4rcx-xphc","Warn: Project is vulnerable to: PYSEC-2021-857 / GHSA-f7c7-j99h-c22f","Warn: Project is vulnerable to: GHSA-fpfv-jqm9-f5jm","Warn: Project is vulnerable to: PYSEC-2017-1 / GHSA-frgw-fgh6-9g52"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}}]},"last_synced_at":"2025-08-21T08:10:16.364Z","repository_id":8612641,"created_at":"2025-08-21T08:10:16.364Z","updated_at":"2025-08-21T08:10:16.364Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279008837,"owners_count":26084517,"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","status":"online","status_checked_at":"2025-10-11T02:00:06.511Z","response_time":55,"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":["cellblender","mcell","simulation"],"created_at":"2024-11-07T07:34:03.316Z","updated_at":"2025-10-11T21:39:46.784Z","avatar_url":"https://github.com/mcellteam.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MCell\n\n## Overview\n\nMCell (Monte Carlo Cell) development is supported by the NIGMS-funded\n(P41GM103712) National Center for Multiscale Modeling of Biological Systems\n(MMBioS).\n\nMCell is a program that uses spatially realistic 3D cellular models and\nspecialized Monte Carlo algorithms to simulate the movements and reactions of\nmolecules within and between cells—cellular microphysiology. \n\n## Build Requirements:\n\n### Ubuntu 16.04:\n\nRun the following commands:\n\n    sudo apt-get update\n    sudo apt-get install cmake build-essential bison flex python3-dev swig libboost-all-dev\n\n### Windows\n\nInstall the package manager chocolatey from https://chocolatey.org/install.\nFollow the instructions listed on that page, which will have you copy a command\ninto PowerShell as an Administrator.\n\nOnce chocolatey is installed, open up a new PowerShell terminal as an\nAdministrator, and run the following commands:\n\n    choco install -y git\n    choco install -y python3\n    choco install -y cmake\n    choco install -y ninja\n    choco install -y msys2\n    choco install -y winflexbison\n    choco install -y swig\n    \nOpen a new PowerShell Administrator terminal and enter the following:\n\n    msys2\n\nThis will open a different MSYS2 terminal (not a PowerShell terminal). In this\nMSYS2 terminal, enter the following commands:\n\n    pacman -Syuu\n    pacman -S --needed base-devel mingw-w64-i686-toolchain mingw-w64-x86_64-toolchain \\\n                    git subversion mercurial \\\n                    mingw-w64-i686-cmake mingw-w64-x86_64-cmake\n    pacman -Sy mingw-w64-i686-boost mingw-w64-x86_64-boost\n\nAdd CMake and MinGW64 to your [Windows PATH Environment\nVariable](https://helpdeskgeek.com/windows-10/add-windows-path-environment-variable/).\nIf you have installed these dependencies with Chocolatey and your top level\ndrive is named `C:`, you can append (or prepend) the following paths into your\nWindows PATH (Search \"Control Panel\"; View by small icons; System; Advanced System Settings;\n              Environment Variables; User Variables; Path; Edit):\n\n    C:\\tools\\msys64\\mingw64\\bin\n    C:\\Program Files\\CMake\\bin\n\n## Building MCell Executable from Source (OSX, Linux, Windows)\n\nOpen a terminal (non-Administrator PowerShell for Windows users), clone the\nmcell_tools repo and run:\n\n    git clone https://github.com/mcellteam/mcell_tools.git\n    cd mcell_tools\n    python3 run.py\n\nThis will clone all the required repositories and run build of all the components.\nRunning 'python3 run.py --help' shows other options.\n\nTo build just MCell, run these commands after you ran the 'python run.py'.\n\n    cd mcell_tools/work/build_mcell\n    cmake ../../../mcell -DCMAKE_BUILD_TYPE=Release\n    make \n\n### Testing MCell\n\n    cd mcell_tests\n    python3 run_tests.py\n\nRunning 'python3 run_tests.py --help' shows other options. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmcellteam%2Fmcell","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmcellteam%2Fmcell","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmcellteam%2Fmcell/lists"}