VirtualMicrobes

Release 0.2.5

Virtual Microbe Evolutionary Simulator

Homepage PyPI Python

License
MIT
Install
pip install VirtualMicrobes==0.2.5

Documentation

VirtualMicrobes

VirtualMicrobes is a scientific Python package that can be used to do in silico evolutionary experiments with Virtual Microbes.

Features

  • individual based, spatially extended model
  • explicit model of genome evolution
  • gene regulatory network
  • metabolic pathways
  • cell growth and division
  • variable, heterogeneous environment

Dependencies

Quick Start

pip install VirtualMicrobes

cd simulation_dir

virtualmicrobes.py evo --name MyFirstMicrobes


Then direct firefox to file://.../simulation_dir/MyFirstMicrobes/00_webapplication.html to observe the evolutionary trajectory of the population.

Custom initialization

cd custom_sim

cp <INSTALL_LOCATION>/src/config_files/example_setup/* custom_sim

virtualmicrobes.py --env-from-file custom_sim/environment.env @custom_sim/general_options.cfg evo @custom_sim/evo_options.cfg --cells-from-files custom_sim/cell_1.cell custom_sim/cell_WGD.cell --name MyCustomMicrobes

Again, observe the evolution of your microbes by directing firefox to file://.../custom_sim/MyCustomMicrobes/00_webapplication.html.

help

  • virtualmicrobes.py --help
  • virtualmicrobes.py evo --help

Documentation

A full description of the model is available here: https://bitbucket.org/thocu/virtualmicrobes/raw/develop/docs/virtual_microbes_methods.pdf

Further help with installing and documentation can be found on http://virtualmicrobes.readthedocs.io/en/latest/

Stats

Dependencies
0
Dependent packages
0
Dependent repositories
0
Total releases
12
Latest release
First release
Forks
0
Watchers
1
Contributors
0
Repository size
71.4 MB
SourceRank
7

Development practices

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Releases

0.2.5
0.2.4
0.2.3
0.2.2
0.2.1
0.2.0
0.1.9
0.1.8
0.1.7
0.1.6
See all 12 releases

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