clovars 0.1.4a0

Clonal Variability Simulation

CloVarS: a clonal variability simulation

This repository contains the source code accompanying the article "CloVarS: a simulation of clonal variability in single cells" (in preparation).

What is CloVarS

The Clonal Variability Simulation (CloVarS) is a cell culture simulation that generates synthetic single-cell lineage data, as normally obtained from time-lapse microscopy experiments.

The example below depicts a single colony, starting from a single cell, which grows over 7 days:

Installation

CloVarS requires Python version 3.8+ in order to run. You can install CloVarS in your Python environment with the command:

pip install clovars

This adds the clovars command to your Python environment, and also installs the necessary dependencies.

How to use CloVarS

CloVarS can be executed in the following modes:

• run - run a simulation with the given settings;
• view - visualize the results of a previous simulation run (figures, images, videos);
• analyse - run analytical tools on the result of a previous simulation run.

You also need to provide the necessary settings files. These files use the TOML syntax, which makes it easy to open and edit them in any text editor.

This folder has examples for the structure of the settings files. Be sure to use them: CloVarS will likely run into errors if the setting files have incorrect or missing values!

For more information on the settings and their meaning, please read the docs here.

Run

clovars run <path-to-run-settings-file> <path-to-colonies-file>

where:

• path-to-run-settings is the path for a TOML file with the run settings;
• path-to-colonies is the path for a TOML file with the colony description.

View

clovars view <path-to-view-settings-file>

where:

• path-to-view-settings is the path for a TOML file with the view settings.

Analyse

clovars analyse <path-to-analysis-settings-file>

where:

• path-to-analysis-settings is the path for a TOML file with the analysis settings.

Fitting experimental data (WIP)

You will be able to fit experimental data to CloVarS's distributions using the command:

clovars fit <path-to-table-file>

Dependencies

CloVarS depends on the following third-party packages:

• ete3
• matplotlib
• numpy
• pandas
• scipy
• seaborn

License

CloVarS is distributed under the MIT license. Read the LICENSE.md file for details.

Cite us

If you use CloVarS, cite us: Faccioni, JL; Lenz, G. (in preparation).