clonalEvolution 2.2.1

Software for simulating clonal evolution in binned and tau leap version.

Introduction

Python software for simulating celluar/microbial clonal evolution with Gillespie algorithm usage

Installation and Usage

The simpliest installation:

python -m pip install microbialClonalEvolution

Usage in python:

from microbialClonalEvolution import mainView
mainView.run()

Usage from console:

python -m clonalEvolution 
#   for simply run graphic verion of software

python -m clonalEvolution -h
#   to see instructions for command line parametrization

Usage Instructions

General Tab:

\

file name - used in multiple functions: saving files, plots, parameters; specify name of file (according to windows acceptable characters), data files will have cycle number (name_number.csv/.txt)
file path - used in multiple functions: saving files, plots, parameters; specify absolute path to folder where simulation data should be saved
file description - 'TODO' add description in params/data file about simulation specyfied by user

clone diagram - button, fire the muller plot creation. It is needed to specify path with muller plot data generated from simulaiton
file structure (file-name_muller_plot_'binned'_data.txt):

clone, cells, previous clone
(0, 5000, 0)

mutations histograms - button, fire the VAF plot creation for all clones in specified file. File is needed to be one of generated simulation data
file structure (file-name_cycle.csv/.txt):

,Clone number,Cells number,Mean fitness,Mean mutation number,Driver mutation list,Passener mutation list,Previous clone number
0,0,5000,1,0,[],[],0

Generated tab:

select which files should be saved automaticaly after one cycle specified in parameters (skip). Not all types works for both algorithm versions 'TODO'

Parameters tab:

Plot tab:

Threads tab:

Main controls:

License

GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc. https://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

Disclaimer

Cellular/Microbial Clonal Evolution simulations basing on Gillespie algorithm. Copyright (C) 2022 by Jarosław Gil

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Author

Jarosław Gil, Silesian Univeristy of Technology, Department of Computer Graphics, Vision and Digital Systems.

Changelog

v1.0.0 - Working single cell algorithm, binned algorithm
v1.1.0 - fixes
v1.1.5 - fixes
v1.2.0 - Added matrix algorithm, process solution (instead of thred, one simulation wokring as new process - much faster)
v1.3.0 - Changed matrix algorithm for more precise caluclations (still warnings and errors can occure)
v1.3.5 - Added time reporting, fixes for matrix algorithm
v1.4.0 - Added plotting methods: fitness wave, clone plot, mutation wave. Fixed VAF histograms method
v1.4.5 - Fixes in threading management
v1.5.0 - Working threading management, plotting