Simulation, analysis, and visualization for subcellular models
Use this installation method for a general user environment. Note that with the installation, you cannot add/remove/update dependencies.
- Create a virtual environment:
conda create -n subcell_pipeline python=3.10 - Activate the environment:
conda activate subcell_pipeline - Install all dependencies:
make install
Or,
- Create a virtual environment:
conda create -n subcell_pipeline python=3.10 - Activate the environment:
conda activate subcell_pipeline - Install conda-specific dependencies:
conda env update --file environment.yml --prune - Install dependencies:
pip install -r requirements.txt - Install the project in editable mode:
pip install -e .
Use this installation method for a complete development environment.
- Create a virtual environment:
conda create -n subcell_pipeline python=3.10 - Activate the environment:
conda activate subcell_pipeline - Install all dependencies:
make install DEV=1
Or,
- Create a virtual environment:
conda create -n subcell_pipeline python=3.10 - Activate the environment:
conda activate subcell_pipeline - Install conda-specific dependencies:
conda env update --file environment.yml --prune - Install dependencies:
pdm sync
Use this installation method for a (mostly) complete, non-Conda development environment.
Note that this installation method does not include the readdy package for ReaDDy-specific post-processsing; if needed, use a conda installation method.
- Install Python 3.10 or higher with
pyenv - Install dependencies:
pdm sync - Activate the environment:
source .venv/bin/activate
The repository contains three major pipeline modules: simulation, analysis, and visualization.
The simulation module contains code for initializing, simulating, and post-processing simulations from different simulators.
The module is further organized by simulator.
- simulation.cytosim -- Simulations and processing for cytoskeleton simulation engine Cytosim
- simulation.readdy -- Simulations and processing for particle-based reaction-diffusion simulator ReaDDy
The analysis module contains code for different analyses.
Each analysis type contains a README with additional information:
- analysis.compression_metrics -- Analysis and plotting for compression metrics on individual fiber shapes
- analysis.dimensionality_reduction -- Analysis and plotting for dimensionality reduction on individual fiber shapes
- analysis.tomography_data -- Processing and analysis of cryo-electron tomography data
- analysis.wall_clock_time -- Analysis of simulation wall clock times
The visualization module contains code for visualizing simulation and analysis outputs.
Definitions of some terms used in this repo.
-
polymer trace
Refers to the line traced by a polymer backbone in three dimensions. For Cytosim, this corresponds to the positions of the control points. For ReaDDy, this corresponds to a derived metric that traces the polymer backbone
-
end-to-end axis
Refers to the line connecting the first and last points of a polymer trace