cellsystem 0.1.0

Example

A use case integrated in the repository:

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)

# 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)
...
...
...

# 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()

# 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)

# 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)

For more examples and usage, please refer to the [Wiki](wikigoeshere.com).

Meta

Ad115 – @Andresio115 – a.garcia230395@gmail.com

Distributed under the MIT license. See 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 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.