Package: clovars
CloVarS: a simulation of single-cell clonal variabilityThis repository contains the source code accompanying the article "CloVarS: a simulation of single-cell clonal variability" (in preparation).What is CloVarSTheClonalVariabilitySimulation (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:QuickstartConfirm that you have Python 3.8 or newer installed in your computerOpen a terminal/CMDType the commandpip install clovarsto download and install CloVarSTypeclovars runto run CloVarS with the default settingsSimulation results are placed in the folder namedoutput(placed in the folder where your terminal is at)InstallationCloVarS requiresPython version 3.8+in order to run. You can install CloVarS in your Python environment with the command:pipinstallclovarsNote: this is meant to be typed in your system terminal / CMD,notin the Python shell.Once installation is complete, theclovarscommand is added yo your system. All necessarydependenciesare installed automatically.How to use CloVarSCloVarS 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;fit- fit experimental data to a variety of curves.You also need to provide the path to the necessarysettings filesas a command-line argument. If no arguments are provided, clovars will use thedefault settings files. These files are set up for demonstration purposes, so we encourage you to use your own when designing new simulations to run.Simulation SettingsThe settings files use theTOMLsyntax, which makes it easy to open and edit them in any text editor.This folderhas examples for the structure of the settings files. Be sure to pay attention: CloVarS will likelyrun into errorsif the setting files haveincorrect or missing values!For more information on the settings and their meaning, pleaseread the docs here(coming soon!).Run CloVarSclovarsrunpath_to/run_settings.tomlpath_to/colonies.tomlwhere:path_to/run_settings.tomlis the path for a TOML file with the run settings;path_to/colonies.tomlis the path for a TOML file describing the colonies to simulate.View CloVarS resultsclovarsviewpath_to/view_settings.tomlwhere:path_to/view_settings.tomlis the path for a TOML file with the view settings.Analyse CloVarS resultsclovarsanalysepath_to/analysis_settings.tomlwhere:path_to/analysis_settings.tomlis the path for a TOML file with the analysis settings.Fit experimental data to treatmentsclovarsfitpath_to/fit_settings.tomlwhere:path_to/fit_settings.tomlis the path for a TOML file with the fit settings.Please refer tothe examples folderfor examples on how the experimental data should be formatted.Troubleshooting / FAQWhen I use the commandpip install clovars, I get the error messageERROR: No matching distribution found for clovarsPlease make sure that you're using Python version 3.8 or newer when trying topip install clovars. You can check your Python version by writing the commandpython --versionin the terminal/CMD.DependenciesCloVarS depends on the following third-party Python packages:ete3matplotlibnumpypandasscipyseabornLicenseCloVarS is distributed under the MIT license. Read theLICENSE.mdfile for details.Cite usIf you use CloVarS, cite us:Juliano L. Faccioni, Julieti H. Buss, Karine R. Begnini, Leonardo G. Brunnet, Manuel M. Oliveira and Guido Lenz. CloVarS: a simulation of single-cell clonal variability (in preparation).