aadarshraghunathan/subcell-analysis

Analysis functionality for subcellar models

subcell-analysis

Analysis functionality for subcellular models

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Installation

Stable Release: pip install subcell-analysis
Development Head: pip install git+https://github.com/Simularium/subcell-analysis.git

Prerequisite

1. Install Conda: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html

Setup

1. create a virtual env: conda create -n subcell_analysis
2. conda activate subcell_analysis
3. conda install readdy==2.0.9
4. pip install -e '.[lint,test,docs,dev]'

**Note: just install will not install readdy correctly, which is needed for tests to pass.

Documentation

For full package documentation please visit Simularium.github.io/subcell-analysis.

Development

See CONTRIBUTING.md for information related to developing the code.

Glossary of terms

Definitions of some terms used in these analyses

• 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

Apache Software License 2.0