# Vivarium Core
[](https://pypi.org/project/vivarium-core/)
[](https://vivarium-core.readthedocs.io/en/latest/)
[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pylint.yml?query=branch%3Amaster)
[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pytest.yml?query=branch%3Amaster)
[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/mypy.yml?query=branch%3Amaster)
Vivarium Core provides a process interface and simulation engine for composing
and executing integrative multi-scale models.
## Getting Started
Vivarium Core is available on PyPI [here](https://pypi.org/project/vivarium-core/), and can be installed as a python library like this:
```console
$ pip install vivarium-core
```
To get started using Vivarium Core, see our
[documentation](https://vivarium-core.readthedocs.io/en/latest/getting_started.html)
and [tutorial
notebooks](https://vivarium-core.readthedocs.io/en/latest/tutorials/index.html).
If you want to contribute to Vivarium Core, see our [contribution
guidelines](https://github.com/vivarium-collective/vivarium-core/blob/master/CONTRIBUTING.md).
## Concept
Computational systems biology requires software for multi-algorithmic model
composition, which allows many modeling efforts to be extended, combined, and
simulated together. We need an "interface protocol" -- analogous to TCP/IP for
the Internet -- which allows diverse pieces of simulation software to connect,
communicate, and synchronize seamlessly into large, complex, and open-ended
networks that anyone can contribute to.
Vivarium addresses the challenges of model reuse and multi-scale integration by
explicitly separating the interface that connects models from the frameworks that
implement them. Vivarium's modular interface makes individual simulation tools into
modules that can be wired together in composite multi-scale models, parallelized
across multiple CPUs, and run with Vivarium's discrete-event simulation engine.
The figure below illustrates the key terminology of Vivarium's interface.
* (**a**) A *Process*, shown as a rectangular flowchart symbol, is a modular model that contains parameters,
an update function, and ports.
* (**b**) A *Store*, shown as the flowchart symbol for a database, holds the state variables and schemas that
determine how to handle updates.
* (**c**) *Composites* are bundles of Processes and Stores wired together by a bipartite network called a *Topology*,
with Processes connecting to Stores through their ports.
* (**d**) *Compartments* are Stores with inner sub-Stores and Processes. Processes can connect across compartments via
boundary stores.
* (**e**) Compartments are embedded in a *Hierarchy* -- depicted as a place network with discrete layers,
with outer compartments shown above and inner compartments below.
<p align="center">
<img src="https://github.com/vivarium-collective/vivarium-core/blob/master/doc/_static/interface.png?raw=true" width="500">
</p>
## License
Copyright (C) 2019-2022 The Vivarium Authors
Licensed under the Apache License, Version 2.0 (the "License"); you may
not use this project except in compliance with the License. You may
obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0.
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
See [`LICENSE.txt`](https://github.com/vivarium-collective/vivarium-core/blob/master/LICENSE.txt) for a copy of the full license, and see
[`AUTHORS.md`](https://github.com/vivarium-collective/vivarium-core/blob/master/AUTHORS.md) for a list of the Vivarium Authors.
Raw data
{
"_id": null,
"home_page": "https://github.com/vivarium-collective/vivarium-core",
"name": "vivarium-core",
"maintainer": null,
"docs_url": null,
"requires_python": "<3.14,>=3.10",
"maintainer_email": null,
"keywords": "vivarium multi-scale computational-biology biology simulation framework",
"author": "Eran Agmon, Ryan Spangler",
"author_email": "eagmon@stanford.edu, ryan.spangler@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/3e/87/794e0b4c5dccbca3036152fe5df56860a57e70f3e68ac0198dbd7df60fcb/vivarium-core-1.6.5.tar.gz",
"platform": null,
"description": "# Vivarium Core\n\n[](https://pypi.org/project/vivarium-core/)\n[](https://vivarium-core.readthedocs.io/en/latest/)\n[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pylint.yml?query=branch%3Amaster)\n[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pytest.yml?query=branch%3Amaster)\n[](https://github.com/vivarium-collective/vivarium-core/actions/workflows/mypy.yml?query=branch%3Amaster)\n\n\nVivarium Core provides a process interface and simulation engine for composing \nand executing integrative multi-scale models.\n\n## Getting Started\n\nVivarium Core is available on PyPI [here](https://pypi.org/project/vivarium-core/), and can be installed as a python library like this:\n\n```console\n$ pip install vivarium-core\n```\n\nTo get started using Vivarium Core, see our\n[documentation](https://vivarium-core.readthedocs.io/en/latest/getting_started.html)\nand [tutorial\nnotebooks](https://vivarium-core.readthedocs.io/en/latest/tutorials/index.html).\n\nIf you want to contribute to Vivarium Core, see our [contribution\nguidelines](https://github.com/vivarium-collective/vivarium-core/blob/master/CONTRIBUTING.md).\n\n## Concept\n\nComputational systems biology requires software for multi-algorithmic model \ncomposition, which allows many modeling efforts to be extended, combined, and \nsimulated together. We need an \"interface protocol\" -- analogous to TCP/IP for \nthe Internet -- which allows diverse pieces of simulation software to connect, \ncommunicate, and synchronize seamlessly into large, complex, and open-ended \nnetworks that anyone can contribute to.\n\nVivarium addresses the challenges of model reuse and multi-scale integration by \nexplicitly separating the interface that connects models from the frameworks that \nimplement them. Vivarium's modular interface makes individual simulation tools into \nmodules that can be wired together in composite multi-scale models, parallelized \nacross multiple CPUs, and run with Vivarium's discrete-event simulation engine.\n\nThe figure below illustrates the key terminology of Vivarium's interface.\n* (**a**) A *Process*, shown as a rectangular flowchart symbol, is a modular model that contains parameters, \nan update function, and ports.\n* (**b**) A *Store*, shown as the flowchart symbol for a database, holds the state variables and schemas that \ndetermine how to handle updates. \n* (**c**) *Composites* are bundles of Processes and Stores wired together by a bipartite network called a *Topology*, \nwith Processes connecting to Stores through their ports. \n* (**d**) *Compartments* are Stores with inner sub-Stores and Processes. Processes can connect across compartments via \nboundary stores.\n* (**e**) Compartments are embedded in a *Hierarchy* -- depicted as a place network with discrete layers, \nwith outer compartments shown above and inner compartments below.\n\n<p align=\"center\">\n <img src=\"https://github.com/vivarium-collective/vivarium-core/blob/master/doc/_static/interface.png?raw=true\" width=\"500\">\n</p>\n\n\n## License\n\nCopyright (C) 2019-2022 The Vivarium Authors\n\nLicensed under the Apache License, Version 2.0 (the \"License\"); you may\nnot use this project except in compliance with the License. You may\nobtain a copy of the License at\nhttp://www.apache.org/licenses/LICENSE-2.0.\n\nUnless required by applicable law or agreed to in writing, software\ndistributed under the License is distributed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\nSee the License for the specific language governing permissions and\nlimitations under the License.\n\nSee [`LICENSE.txt`](https://github.com/vivarium-collective/vivarium-core/blob/master/LICENSE.txt) for a copy of the full license, and see\n[`AUTHORS.md`](https://github.com/vivarium-collective/vivarium-core/blob/master/AUTHORS.md) for a list of the Vivarium Authors.\n\n\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "Engine for composing and simulating computational biology models with the Vivarium interface.",
"version": "1.6.5",
"project_urls": {
"Changelog": "https://github.com/vivarium-collective/vivarium-core/blob/master/CHANGELOG.md",
"Documentation": "https://vivarium-core.readthedocs.io/en/latest/",
"Homepage": "https://github.com/vivarium-collective/vivarium-core",
"Source": "https://github.com/vivarium-collective/vivarium-core"
},
"split_keywords": [
"vivarium",
"multi-scale",
"computational-biology",
"biology",
"simulation",
"framework"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "3e87794e0b4c5dccbca3036152fe5df56860a57e70f3e68ac0198dbd7df60fcb",
"md5": "961db4db700c8600e1fba493b3bd842f",
"sha256": "1d83faa60005304b548f623447ab8675a06bb7ed8f6b7c0bd25b4aaa3381fccb"
},
"downloads": -1,
"filename": "vivarium-core-1.6.5.tar.gz",
"has_sig": false,
"md5_digest": "961db4db700c8600e1fba493b3bd842f",
"packagetype": "sdist",
"python_version": "source",
"requires_python": "<3.14,>=3.10",
"size": 136102,
"upload_time": "2024-12-03T21:49:29",
"upload_time_iso_8601": "2024-12-03T21:49:29.797684Z",
"url": "https://files.pythonhosted.org/packages/3e/87/794e0b4c5dccbca3036152fe5df56860a57e70f3e68ac0198dbd7df60fcb/vivarium-core-1.6.5.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-12-03 21:49:29",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "vivarium-collective",
"github_project": "vivarium-core",
"travis_ci": false,
"coveralls": true,
"github_actions": true,
"requirements": [
{
"name": "matplotlib",
"specs": [
[
"==",
"3.9.3"
]
]
},
{
"name": "networkx",
"specs": [
[
"==",
"3.4.2"
]
]
},
{
"name": "numpy",
"specs": [
[
"==",
"2.1.3"
]
]
},
{
"name": "Pint",
"specs": [
[
"==",
"0.24.4"
]
]
},
{
"name": "pymongo",
"specs": [
[
"==",
"4.10.1"
]
]
},
{
"name": "scipy",
"specs": [
[
"==",
"1.14.1"
]
]
},
{
"name": "orjson",
"specs": [
[
"==",
"3.10.12"
]
]
},
{
"name": "mypy",
"specs": [
[
"==",
"1.13.0"
]
]
},
{
"name": "mypy-extensions",
"specs": [
[
"==",
"1.0.0"
]
]
},
{
"name": "pylint",
"specs": [
[
"==",
"3.3.2"
]
]
},
{
"name": "pytest",
"specs": [
[
"==",
"8.3.4"
]
]
},
{
"name": "pytest-cov",
"specs": [
[
"==",
"6.0.0"
]
]
},
{
"name": "setuptools",
"specs": [
[
"==",
"73.0.1"
]
]
},
{
"name": "Sphinx",
"specs": [
[
"==",
"8.1.3"
]
]
},
{
"name": "sphinx-rtd-theme",
"specs": [
[
"==",
"3.0.2"
]
]
},
{
"name": "alabaster",
"specs": [
[
"==",
"1.0.0"
]
]
},
{
"name": "astroid",
"specs": [
[
"==",
"3.3.5"
]
]
},
{
"name": "asttokens",
"specs": [
[
"==",
"3.0.0"
]
]
},
{
"name": "attrs",
"specs": [
[
"==",
"24.2.0"
]
]
},
{
"name": "babel",
"specs": [
[
"==",
"2.16.0"
]
]
},
{
"name": "backcall",
"specs": [
[
"==",
"0.2.0"
]
]
},
{
"name": "beautifulsoup4",
"specs": [
[
"==",
"4.12.3"
]
]
},
{
"name": "bleach",
"specs": [
[
"==",
"6.2.0"
]
]
},
{
"name": "certifi",
"specs": [
[
"==",
"2024.8.30"
]
]
},
{
"name": "charset-normalizer",
"specs": [
[
"==",
"3.4.0"
]
]
},
{
"name": "contourpy",
"specs": [
[
"==",
"1.3.1"
]
]
},
{
"name": "coverage",
"specs": [
[
"==",
"7.6.8"
]
]
},
{
"name": "cycler",
"specs": [
[
"==",
"0.12.1"
]
]
},
{
"name": "decorator",
"specs": [
[
"==",
"5.1.1"
]
]
},
{
"name": "defusedxml",
"specs": [
[
"==",
"0.7.1"
]
]
},
{
"name": "dill",
"specs": [
[
"==",
"0.3.9"
]
]
},
{
"name": "dnspython",
"specs": [
[
"==",
"2.7.0"
]
]
},
{
"name": "docutils",
"specs": [
[
"==",
"0.21.2"
]
]
},
{
"name": "executing",
"specs": [
[
"==",
"2.1.0"
]
]
},
{
"name": "fastjsonschema",
"specs": [
[
"==",
"2.21.0"
]
]
},
{
"name": "flexcache",
"specs": [
[
"==",
"0.3"
]
]
},
{
"name": "flexparser",
"specs": [
[
"==",
"0.4"
]
]
},
{
"name": "fonttools",
"specs": [
[
"==",
"4.55.0"
]
]
},
{
"name": "idna",
"specs": [
[
"==",
"3.10"
]
]
},
{
"name": "imagesize",
"specs": [
[
"==",
"1.4.1"
]
]
},
{
"name": "importlib_metadata",
"specs": [
[
"==",
"8.5.0"
]
]
},
{
"name": "iniconfig",
"specs": [
[
"==",
"2.0.0"
]
]
},
{
"name": "ipython",
"specs": [
[
"==",
"8.30.0"
]
]
},
{
"name": "isort",
"specs": [
[
"==",
"5.13.2"
]
]
},
{
"name": "jedi",
"specs": [
[
"==",
"0.19.2"
]
]
},
{
"name": "Jinja2",
"specs": [
[
"==",
"3.1.4"
]
]
},
{
"name": "jsonschema",
"specs": [
[
"==",
"4.23.0"
]
]
},
{
"name": "jsonschema-specifications",
"specs": [
[
"==",
"2024.10.1"
]
]
},
{
"name": "jupyter_client",
"specs": [
[
"==",
"8.6.3"
]
]
},
{
"name": "jupyter_core",
"specs": [
[
"==",
"5.7.2"
]
]
},
{
"name": "jupyterlab_pygments",
"specs": [
[
"==",
"0.3.0"
]
]
},
{
"name": "kiwisolver",
"specs": [
[
"==",
"1.4.7"
]
]
},
{
"name": "lazy-object-proxy",
"specs": [
[
"==",
"1.10.0"
]
]
},
{
"name": "MarkupSafe",
"specs": [
[
"==",
"3.0.2"
]
]
},
{
"name": "matplotlib-inline",
"specs": [
[
"==",
"0.1.7"
]
]
},
{
"name": "mccabe",
"specs": [
[
"==",
"0.7.0"
]
]
},
{
"name": "mistune",
"specs": [
[
"==",
"3.0.2"
]
]
},
{
"name": "nbclient",
"specs": [
[
"==",
"0.10.1"
]
]
},
{
"name": "nbconvert",
"specs": [
[
"==",
"7.16.4"
]
]
},
{
"name": "nbformat",
"specs": [
[
"==",
"5.10.4"
]
]
},
{
"name": "nbsphinx",
"specs": [
[
"==",
"0.9.5"
]
]
},
{
"name": "packaging",
"specs": [
[
"==",
"24.2"
]
]
},
{
"name": "pandocfilters",
"specs": [
[
"==",
"1.5.1"
]
]
},
{
"name": "parso",
"specs": [
[
"==",
"0.8.4"
]
]
},
{
"name": "pexpect",
"specs": [
[
"==",
"4.9.0"
]
]
},
{
"name": "pickleshare",
"specs": [
[
"==",
"0.7.5"
]
]
},
{
"name": "pillow",
"specs": [
[
"==",
"11.0.0"
]
]
},
{
"name": "platformdirs",
"specs": [
[
"==",
"4.3.6"
]
]
},
{
"name": "pluggy",
"specs": [
[
"==",
"1.5.0"
]
]
},
{
"name": "prompt_toolkit",
"specs": [
[
"==",
"3.0.48"
]
]
},
{
"name": "ptyprocess",
"specs": [
[
"==",
"0.7.0"
]
]
},
{
"name": "pure_eval",
"specs": [
[
"==",
"0.2.3"
]
]
},
{
"name": "py",
"specs": [
[
"==",
"1.11.0"
]
]
},
{
"name": "Pygments",
"specs": [
[
"==",
"2.18.0"
]
]
},
{
"name": "pyparsing",
"specs": [
[
"==",
"3.2.0"
]
]
},
{
"name": "pyrsistent",
"specs": [
[
"==",
"0.20.0"
]
]
},
{
"name": "python-dateutil",
"specs": [
[
"==",
"2.9.0.post0"
]
]
},
{
"name": "pytz",
"specs": [
[
"==",
"2024.2"
]
]
},
{
"name": "pyzmq",
"specs": [
[
"==",
"26.2.0"
]
]
},
{
"name": "referencing",
"specs": [
[
"==",
"0.35.1"
]
]
},
{
"name": "requests",
"specs": [
[
"==",
"2.32.3"
]
]
},
{
"name": "rpds-py",
"specs": [
[
"==",
"0.21.0"
]
]
},
{
"name": "six",
"specs": [
[
"==",
"1.16.0"
]
]
},
{
"name": "snowballstemmer",
"specs": [
[
"==",
"2.2.0"
]
]
},
{
"name": "soupsieve",
"specs": [
[
"==",
"2.6"
]
]
},
{
"name": "sphinxcontrib-applehelp",
"specs": [
[
"==",
"2.0.0"
]
]
},
{
"name": "sphinxcontrib-devhelp",
"specs": [
[
"==",
"2.0.0"
]
]
},
{
"name": "sphinxcontrib-htmlhelp",
"specs": [
[
"==",
"2.1.0"
]
]
},
{
"name": "sphinxcontrib-jquery",
"specs": [
[
"==",
"4.1"
]
]
},
{
"name": "sphinxcontrib-jsmath",
"specs": [
[
"==",
"1.0.1"
]
]
},
{
"name": "sphinxcontrib-qthelp",
"specs": [
[
"==",
"2.0.0"
]
]
},
{
"name": "sphinxcontrib-serializinghtml",
"specs": [
[
"==",
"2.0.0"
]
]
},
{
"name": "stack-data",
"specs": [
[
"==",
"0.6.3"
]
]
},
{
"name": "tinycss2",
"specs": [
[
"==",
"1.4.0"
]
]
},
{
"name": "toml",
"specs": [
[
"==",
"0.10.2"
]
]
},
{
"name": "tomli",
"specs": [
[
"==",
"2.2.1"
]
]
},
{
"name": "tomlkit",
"specs": [
[
"==",
"0.13.2"
]
]
},
{
"name": "tornado",
"specs": [
[
"==",
"6.4.2"
]
]
},
{
"name": "traitlets",
"specs": [
[
"==",
"5.14.3"
]
]
},
{
"name": "typing_extensions",
"specs": [
[
"==",
"4.12.2"
]
]
},
{
"name": "urllib3",
"specs": [
[
"==",
"2.2.3"
]
]
},
{
"name": "wcwidth",
"specs": [
[
"==",
"0.2.13"
]
]
},
{
"name": "webencodings",
"specs": [
[
"==",
"0.5.1"
]
]
},
{
"name": "wrapt",
"specs": [
[
"==",
"1.17.0"
]
]
},
{
"name": "zipp",
"specs": [
[
"==",
"3.21.0"
]
]
}
],
"lcname": "vivarium-core"
}
