Clonal Variability Simulation
Project description
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. CloVarS will likely run into errors if the setting files have missing / wrong values!
Run CloVarS
clovars run <path-to-run-settings> <path-to-colonies>
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
clovars view <path-to-view-settings>
where:
path-to-view-settings
is the path for a TOML file with the view settings.
Analyse CloVarS
clovars analyse <path-to-analysis-settings>
where:
path-to-analysis-settings
is the path for a TOML file with the analysis settings.
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).
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