Run ReaDDy no compression simulations¶

Notebook contains steps for running ReaDDy simulations for a baseline single actin fiber with no compression.

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_NO_COMPRESSION simulation series, which simulates a single actin fiber with a free barbed end across five replicates.

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

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

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

# Number of simulation replicates
n_replicates: int = 5

Copy simulation outputs¶

copy_simulation_outputs(bucket, series_name, source_template, n_replicates)