Metadata-Version: 1.1
Name: cellsystem
Version: 0.1.0
Summary: An agent-based framework for the simulation of biological cell systems and more.
Home-page: https://github.com/Ad115/Cell-System
Author: Ad115
Author-email: a.garcia230395@gmail.com
License: UNKNOWN
Description-Content-Type: UNKNOWN
Description: ==========
        CellSystem
        ==========
        
        https://saythanks.io/inbox#badge-modal
        
        An agent-based framework for the simulation of biological cell systems (although it could conceivably do more).
        
        This was created to simulate cancer growth, taking into account nutrients and cell migration while allowing to couple mutations and ancestry logging to study tumour phylogeny reconstruction algorithms.
        
        .. image:: https://raw.githubusercontent.com/Ad115/Cell-System/master/assets/sidebyside.png
        .. image:: https://raw.githubusercontent.com/Ad115/Cell-System/master/assets/spacetime.png
        
        -------
        Example
        -------
        
        A use case integrated in the repository:
        
        .. code-block:: python
        
            from cellsystem import *
        
            # The cell system will simulate cell growth
            # while tracking the steps in that process.
            system = CellSystem(grid_dimensions=(10, 10))
        
            # Initialize the first cell
            # in the middle of the grid
            system.seed()
        
        ::
        
            New cell 0 added @ (5, 5)
                
        .. code-block:: python
        
            # Take 35 steps forward in time
            system.run(steps=30)
            
        ::
        
            Cell no. 0 dividing @ (5, 5)
            New cells: 2 @ (4, 5) and 1 @ (6, 6)
            Cell no. 2 mutating @ site (4, 5) (father 0)
                Initial mutations: []
                    Initial genome: AAAAAAAAAA
                Final mutations: [(3, 'C')]
                    Final genome: AAACAAAAAA
            Cell no. 1 dividing @ (6, 6)
                New cells: 4 @ (6, 6) and 3 @ (5, 6)
            Cell no. 2 death @ site (4, 5) (father 0)
            Cell no. 3 migrating from site (5, 6) (father 1)
                New site: (4, 5)
            Cell no. 4 death @ site (6, 6) (father 1)
            Cell no. 3 dividing @ (4, 5)
                New cells: 6 @ (3, 6) and 5 @ (3, 5)
            ...
            ...
            ...
        
        .. code-block:: python
        
            # Prepare to explore the simulation logs
            history = system['log']
        
        
        
            # First, let's see the cells' evolution in time and space!
            history.geometry().show()
        
            # Remove the cells that died somewhere along the way
            history.geometry(prune_death=True).show()
        
        .. image:: https://raw.githubusercontent.com/Ad115/Cell-System/master/assets/worldlines.png
        
        .. image:: https://raw.githubusercontent.com/Ad115/Cell-System/master/assets/worldlines_no_death.png
        
        .. code-block:: python
        
            # Prepare styling for the trees
            tree_style = {'show_leaf_name' : True,
                        'mode' : 'c',        # Circular tree
                        'arc_start' : -135,  # Degrees
                        'arc_span' : 270 }   # Degrees also
        
            # Lookup the tree formed by cellular division
            history.ancestry().show(styling=tree_style)
        
            # Now, remove cells that are no longer alive
            history.ancestry(prune_death=True).show(styling=tree_style)
        
        .. image:: https://raw.githubusercontent.com/Ad115/Cell-System/master/assets/ancestry.png
        
        .. image:: https://raw.githubusercontent.com/Ad115/Cell-System/master/assets/ancestry_no_death.png
        
        .. code-block:: python
        
            # Now, check out the tree formed by the mutations 
            history.mutations().show(styling=tree_style)
        
            # Remove genomes with no living representatives.
            history.mutations(prune_death=True).show(styling=tree_style)
        
        .. image:: https://raw.githubusercontent.com/Ad115/Cell-System/master/assets/mutations.png
        
        .. image:: https://raw.githubusercontent.com/Ad115/Cell-System/master/assets/mutations_no_death.png
        
        
        *For more examples and usage, please refer to the [Wiki](wikigoeshere.com).*
        
        ----
        Meta
        ----
        
        Ad115 – `@Andresio115 <https://twitter.com/Andresio115>`_ – a.garcia230395@gmail.com
        
        Distributed under the MIT license. See `LICENSE <https://github.com/Ad115/Cell-System/blob/master/LICENSE>`_ for more information.
        
        ------------
        Contributing
        ------------
        
        1. Check for open issues or open a fresh issue to start a discussion around a feature idea or a bug.
        2. Fork `the repository <https://github.com/Ad115/Cell-System/>`_ on GitHub to start making your changes to a feature branch, derived from the **master** branch.
        3. Write a test which shows that the bug was fixed or that the feature works as expected.
        4. Send a pull request and bug the maintainer until it gets merged and published. 
        
Keywords: simulation cell agents
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Education
Classifier: Topic :: Scientific/Engineering :: Artificial Life
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3 :: Only
