Metadata-Version: 2.1
Name: VirtualMicrobes
Version: 0.1.7
Summary: Virtual Microbe Evolutionary Simulator
Home-page: https://bitbucket.org/thocu/virtualmicrobes
Author: Thomas D. Cuypers
Author-email: thomas.cuypers@gmail.com
License: UNKNOWN
Description: ***************
        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
        ^^^^^^^^^^^^
        
        - `gsl <https://www.gnu.org/software/gsl/>`_
        - `ete3 <http://etetoolkit.org/>`_ (tree drawing and phylogenetics)
        - `cython <http://cython.org>`_
        - `matplotlib <http://matplotlib.org>`_
        - `networkx <http://networkx.github.io/>`_ (network analysis and drawing)
        - others see requirements.txt
        
        
        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/
        
        CHANGELOG
        ---------
        
        nothing changed here
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Cython
Classifier: Topic :: Scientific/Engineering :: Artificial Life
Classifier: Topic :: Scientific/Engineering
Provides-Extra: testing
