Simulation workflow notebooks¶
Cytosim simulations¶
Simulations and processing for cytoskeleton simulation engine Cytosim.
Base simulator: https://gitlab.com/f-nedelec/cytosim
Model development: https://github.com/simularium/Cytosim
Baseline single actin fiber with no compression¶
The ACTIN_NO_COMPRESSION simulation series simulates a single actin fiber with a free barbed end across five replicates.
Single actin fiber compressed at different compression velocities¶
The ACTIN_COMPRESSION_VELOCITY simulation series simulates compression of a single 500 nm actin fiber at four different velocities (4.7, 15, 47, and 150 μm/s) with five replicates.
ReaDDy simulations¶
Simulations and processing for particle-based reaction-diffusion simulator ReaDDy.
Base simulator: https://github.com/readdy/readdy
Model development: https://github.com/simularium/readdy-models
Baseline single actin fiber with no compression¶
The ACTIN_NO_COMPRESSION simulation series simulates a single actin fiber with a free barbed end across five replicates.
Single actin fiber compressed at different compression velocities¶
The ACTIN_COMPRESSION_VELOCITY simulation series simulates compression of a single 500 nm actin fiber at four different velocities (4.7, 15, 47, and 150 μm/s) with five replicates.