ecoprospector

Simulating protocols for the artificial selection of microbial communities

This package is designed to simulate arbitrary community-level selection protocols on microbial metacommunitities in order to determine whether they can effectively engineer communitities with desired functions. The simulation are based on batch culture and the microbes in each community interact via consumer-resource dynamics.

See our paper that uses ecoprospector to study a range of selection strategies that direct the evolution of microbial communities.

Installation

Anaconda

A python development setup by Anaconda will be sufficient to implement community-simulator and ecoprospector.

Mac and Linux

Install requirement

# Required to build wheel for qdldl
pip install cmake

# Install requirements
pip install -r requirements.txt 

Download the code or clone the github repository of community simulator to a local directory and browse to the community-simulator directory and install the package

cd <your_local_directory>
git clone https://github.com/Emergent-Behaviors-in-Biology/community-simulator

Download the code or clone this github repository to a local directory and browse to the ecoprospector directory and install package

cd <your_local_directory>
git clone https://github.com/Chang-Yu-Chang/ecoprospector
pip install -e .

Windows

The parallelization features in community-simulator are not currently supported on Windows and as such we cannot guarantee that the current version of ecoprospector will work in a windows environment. We would recommend using a linux emulator for windows such as Cygwin instead.

Usage example

With the mapping file (csv), executing one experiment is simple as

$ ecoprospector input_example.csv 0

For more examples and usage, please refer to the documentation.

Release History

• 0.0.3
  • Add requirements file. Solve the syntax issue caused by latest pandas
  • Update README for installing the required packages
  • Provide the input_example.csv
  • Change the commandline tool to lower case
• 0.0.2
  • Include other non-additive functions
• 0.0.1
  • Work in progress

Documentation

Ecoprospector's documentation lives at ecoprospector.readthedocs.io

Meta

Chang-Yu Chang – @changyu_chang – changyuchang5@gmail.com

Jean Vila – @jccvila – Jeanccvila@gmail.com

Distributed under the MIT license. See LICENSE for more information.

https://github.com/Chang-Yu-Chang/ecoprospector