allencellmodeling / flins

Simulate a system of linear filaments

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

flins's Issues

Rename project

Rename the project to myogen as it really is not modeling a stress-fiber any longer.

Create end-anchoring function in `construct` module

Take abs value of dist to get nearest

https://github.com/AllenCellModeling/stress_fiber/blob/87d054841a9723b0c37534da61a5e43ee89c0493/stress_fiber/proteins/alpha_actinin.py#L51

Create JSON or other serialized format-to-world parser

Need to be able to have starting conditions specified in a parameter file. Need that parameter file to be able to be an input to the world for parameterized runs.

Create random actin populating generation

Create order estimation metric

Entropy based or otherwise...