Run ReaDDy compression simulations

Notebook contains steps for running ReaDDy simulations in which a single actin fiber is compressed at different compression velocities.

Simulations use the ReaDDy actin model defined here. Instructions for running this model on AWS Batch are provided here.

After simulations are complete, use this notebook to copy output files into the file structure used by this pipeline.

• Define simulation conditions

• Copy simulation outputs

if __name__ != "__main__":
    raise ImportError("This module is a notebook and is not meant to be imported")

from subcell_pipeline.simulation.batch_simulations import copy_simulation_outputs

Define simulation conditions

Defines the ACTIN_COMPRESSION_VELOCITY simulation series, which compresses a single 500 nm actin fiber at four different velocities (4.7, 15, 47, and 150 μm/s) with five replicates each.

# Name of the simulation series
series_name: str = "ACTIN_COMPRESSION_VELOCITY"

# Template for simulation output files
source_template: str = "outputs/actin_compression_velocity=%s_%d.h5"

# S3 bucket for input and output files
bucket: str = "s3://readdy-working-bucket"

# Number of simulation replicates
n_replicates: int = 5

# File keys for each velocity
velocity_keys: dict[str, str] = {
    "4.7": "0047",
    "15": "0150",
    "47": "0470",
    "150": "1500",
}

Copy simulation outputs

copy_simulation_outputs(
    bucket, series_name, source_template, n_replicates, velocity_keys
)