Metadata-Version: 2.1
Name: vivarium-core
Version: 1.2.0
Summary: Engine for composing and simulating computational biology models with the Vivarium interface.
Home-page: https://github.com/vivarium-collective/vivarium-core
Author: Eran Agmon, Ryan Spangler
Author-email: eagmon@stanford.edu, ryan.spangler@gmail.com
License: MIT
Project-URL: Source, https://github.com/vivarium-collective/vivarium-core
Project-URL: Documentation, https://vivarium-core.readthedocs.io/en/latest/
Project-URL: Changelog, https://github.com/vivarium-collective/vivarium-core/blob/master/CHANGELOG.md
Description: # Vivarium Core
        
        [![PyPI](https://img.shields.io/pypi/v/vivarium-core)](https://pypi.org/project/vivarium-core/)
        [![documentation](https://github.com/vivarium-collective/vivarium-core/actions/workflows/docs.yml/badge.svg)](https://vivarium-core.readthedocs.io/en/latest/)
        [![lint](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pylint.yml/badge.svg)](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pylint.yml?query=branch%3Amaster)
        [![pytest](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pytest.yml/badge.svg)](https://github.com/vivarium-collective/vivarium-core/actions/workflows/pytest.yml?query=branch%3Amaster)
        [![mypy](https://github.com/vivarium-collective/vivarium-core/actions/workflows/mypy.yml/badge.svg)](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.
        
        ## 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>
        
        
        ## Getting Started
        
        Vivarium Core 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
        notebook](https://vivarium-core.readthedocs.io/en/latest/tutorials.html).
        
        If you want to contribute to Vivarium Core, see our [contribution
        guidelines](https://github.com/vivarium-collective/vivarium-core/blob/master/CONTRIBUTING.md).
        
        ## 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.
        
Keywords: vivarium multi-scale computational-biology biology simulation framework
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.8, <3.11
Description-Content-Type: text/markdown
