https://github.com/allencellmodeling/flins

Simulate a system of linear filaments
https://github.com/allencellmodeling/flins

biophysics cell-biology muscle stress-fibers

Last synced: 8 months ago
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Simulate a system of linear filaments

• Host: GitHub
• URL: https://github.com/allencellmodeling/flins
• Owner: AllenCellModeling
• License: other
• Created: 2019-02-05T18:44:41.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2020-01-29T00:13:23.000Z (over 5 years ago)
• Last Synced: 2025-01-02T23:14:21.811Z (9 months ago)
• Topics: biophysics, cell-biology, muscle, stress-fibers
• Language: Python
• Homepage:
• Size: 7.67 MB
• Stars: 0
• Watchers: 5
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • Changelog: HISTORY.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE

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README

          
.. image:: https://raw.githubusercontent.com/AllenCellModeling/flins/master/imgs/logo.png

   :alt: FLINS

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        :target: https://AllenCellModeling.github.io/flins

        :alt: Documentation Status

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Overview

--------

``flins`` is a spatial, agent-based simulation of the movement of actin, cross-linkers, and adhesions in a pre-myofibril. It explores the conditions necessary to generate the emergent organization we see in differentiating and developing muscle cells. 

As a spatially explicit simulation ``flins`` recreates the movement and force responses of its proteins by treating them as springs, subject to deformation and able to generate force with variable rest lengths. Connectivity and binding withing this system of proteins is controlled by binding sites distributed along the proteins that link springs together. The kinetics of these binding sites are dependent upon the forces their parent proteins are subjected to. This produces a network of springs that transmits and generates forces with connectivity that changes depending on stochastic kinetics and the current deformation within the system. 

  

Minimal example::

    import flins

    world = flins.construct.create_test_world(

        radius=1,     # how wide the world is

        span=10000,   # how long

        n_actin=5,    # actins per slice

        n_actinin=20, # crosslinkers per slice

        n_motors=10,  # motors per slice

        )    

    world.step()

* Documentation: https://AllenCellModeling.github.io/flins