{"id":44036845,"url":"https://github.com/virtualcell/vcell-ode","last_synced_at":"2026-02-07T20:08:52.856Z","repository":{"id":297265934,"uuid":"996226252","full_name":"virtualcell/vcell-ode","owner":"virtualcell","description":"The ODE focused solvers VCell utilizes in it's main applications","archived":false,"fork":false,"pushed_at":"2025-12-18T18:05:54.000Z","size":88805,"stargazers_count":0,"open_issues_count":4,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-12-20T07:02:53.404Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/virtualcell.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-06-04T16:31:27.000Z","updated_at":"2025-06-16T15:55:25.000Z","dependencies_parsed_at":"2025-06-30T14:48:45.774Z","dependency_job_id":null,"html_url":"https://github.com/virtualcell/vcell-ode","commit_stats":null,"previous_names":["virtualcell/vcell-ode"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/virtualcell/vcell-ode","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/virtualcell%2Fvcell-ode","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/virtualcell%2Fvcell-ode/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/virtualcell%2Fvcell-ode/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/virtualcell%2Fvcell-ode/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/virtualcell","download_url":"https://codeload.github.com/virtualcell/vcell-ode/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/virtualcell%2Fvcell-ode/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29207129,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-07T17:44:10.191Z","status":"ssl_error","status_checked_at":"2026-02-07T17:44:07.936Z","response_time":63,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2026-02-07T20:08:52.199Z","updated_at":"2026-02-07T20:08:52.846Z","avatar_url":"https://github.com/virtualcell.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\" width=\"100%\"\u003e\n \u003ca href=\"https://vcell.org\"\u003e\n    \u003cimg width=\"10%\" src=\"https://github.com/biosimulations/biosimulations/blob/dev/docs/src/assets/images/about/partners/vcell.svg\"\u003e\n \u003c/a\u003e\n\u003c/p\u003e\n\n## The Virtual Cell Project\nThe Virtual Cell is a modeling and simulation framework for computational biology.  For details see http://vcell.org and http://github.com/virtualcell.\n\n---\n# vcell-ode\n![CI](https://github.com/virtualcell/vcell-ode/actions/workflows/cd.yml/badge.svg)\n\nVirtual Cell ODE [virtualcell/vcell-ode](https://github.com/virtualcell/vcell-ode) is a collection of numerical \nsimulation libraries and protocols used to process ODEs in the Virtual Cell framework [virtualcell/vcell](https://github.com/virtualcell/vcell)).\n\n## Building VCell ODE\nThere are two ways to build VCell ODE, but both start out the same way\n### Step 1: Acquire the source-code\nThe source code can be found online at the GitHub repository.\n`git clone https://github.com/virtualcell/vcell.git`\n\n### Step 2: Install Dependencies \nYou will need to acquire a unix-style C and C++ compiler suite in order to build VCell ODE. Traditionally, this project \nuses CLang + Mold, but other compiler suites may work. Additionally, you'll need to install the other dependencies for \nVCell ODE, which can be done in one of two ways:\n\n#### Method 1: Conan Toolchain (Recommended)\nThe VCell ODE project uses the C++ dependency management system called ***conan*** to handle dependency management when \nbuilding VCell ODE. We provide a number of conan-profiles that will provide conan the information need to automatically \nbuild the desired toolchain for cmake.\n\n#### Method 2: Manual Dependency Installation\nIf you'd rather manually install all the dependencies build-tools to create VCell CLI, you'll need the following:\n##### Dependencies\n* If you want live messaging while the solver runs: `libcurl` (add `-DOPTION_TARGET_MESSAGING` to cmake call below)\n##### Build Tools\n* `cmake` to perform the build configuration\n* `ninja` (or equivalent) to perform the actual build process\n\n### Step 3: Invoke the Build\nIn a shell with conan and/or the other build tools in path, navigate to the project's root directory and \nrun the following commands (tested in bash on unix and powershell on windows)\n\nNote that if using `conan`, you'll need to define a profile. use `conan profile detect --force` to generate one automatically, \nor use one of the provided ones in `\u003cproject_root\u003e/conan-profiles` [link](https://docs.conan.io/2/reference/config_files/profiles.html)\nto further reading on the official `conan` website.\n#### Powershell\n```pwsh\n    mdkir build # Must do if not using conan\n    conan install . --output-folder build --build=missing # If building using conan's help\n    cd build\n    ./conanbuild.ps1 # If building using conan's help\n    cmake -B . -S .. -G \"Ninja\" -DCMAKE_TOOLCHAIN_FILE=\"conan_toolchain.cmake\" -DCMAKE_BUILD_TYPE=Release\n    cmake --build . --config Release\n```\n\n```bash\n    mdkir build # must do if not building conan\n    conan install . --output-folder build --build=missing # If building using conan's help\n    cd build\n    ./conanbuild.sh # If building using conan's help\n    cmake -B . -S .. -G \"Ninja\" -DCMAKE_TOOLCHAIN_FILE=\"conan_toolchain.cmake\" -DCMAKE_BUILD_TYPE=Release\n    cmake --build . --config Release\n```\n\n### Step 4: Manual user/system install\nCurrently, VCell ODE does not have an automated installation script. You will either need to move the resulting executables\nin `\u003cproject_root\u003e/build/bin` to an appropriate folder in path, or put said folder into path for your computer.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvirtualcell%2Fvcell-ode","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvirtualcell%2Fvcell-ode","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvirtualcell%2Fvcell-ode/lists"}