Subcellular model simulation and analysis pipeline

Simulation, analysis, and visualization for subcellular models

---

Installation

Install with conda and pip

Use this installation method for a general user environment. Note that with the installation, you cannot add/remove/update dependencies.

1. Create a virtual environment: conda create -n subcell_pipeline python=3.10

2. Activate the environment: conda activate subcell_pipeline

3. Install all dependencies: make install

Or,

1. Create a virtual environment: conda create -n subcell_pipeline python=3.10

2. Activate the environment: conda activate subcell_pipeline

3. Install conda-specific dependencies: conda env update --file environment.yml --prune

4. Install dependencies: pip install -r requirements.txt

5. Install the project in editable mode: pip install -e .

Install with conda and pdm

Use this installation method for a complete development environment.

1. Create a virtual environment: conda create -n subcell_pipeline python=3.10

2. Activate the environment: conda activate subcell_pipeline

3. Install all dependencies: make install DEV=1

Or,

1. Create a virtual environment: conda create -n subcell_pipeline python=3.10

2. Activate the environment: conda activate subcell_pipeline

3. Install conda-specific dependencies: conda env update --file environment.yml --prune

4. Install dependencies: pdm sync

Install with pyenv and pdm

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.

1. Install Python 3.10 or higher with pyenv

2. Install dependencies: pdm sync

3. Activate the environment: source .venv/bin/activate

Usage

The repository contains three major pipeline modules: simulation, analysis, and visualization.

Simulations

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

Analysis

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

Visualization

The visualization module contains code for visualizing simulation and analysis outputs.

Glossary

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

subcell_pipeline.simulation	Simulation methods and notebooks.
subcell_pipeline.analysis	Analysis methods and notebooks.
subcell_pipeline.visualization	Visualization methods and notebooks.