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Python tools for Synthetic Biology.

Project description

SynBioPython

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SynBiopython provides generic tools for Synthetic Biology. For more details, please see the publication:

SynBiopython: an open-source software library for Synthetic Biology, Jing Wui Yeoh, Neil Swainston, Peter Vegh, Valentin Zulkower, Pablo Carbonell, Maciej B Holowko, Gopal Peddinti, Chueh Loo Poh. Synthetic Biology (2021) ysab001

Installation

pip install synbiopython

To install the latest version from Github:

pip install git+https://github.com/Global-Biofoundries-Alliance/SynBioPython

Currently Python 3.6, 3.7 and 3.8 are supported.

Usage

You should now be able to run this in Python:

import synbiopython
print(synbiopython.__version__)

Currently, there are three modules implemented:

  • The genbabel module provides standard file parsers and for working with multiple fileformats.
  • The codon module provides support for codon optimisation.
  • The lab automation module enables working with plates and generation of picklists (transfers) for liquid handlers.

Examples

Example Jupyter notebooks are provided for each module: codon, genbabel and lab automation. In order to open these notebooks, download and install JupyterLab.

Contribute!

SynBiopython is developed collectively by members of the Global Biofoundry Alliance and released on Github under the MIT license. Contributions are welcome!

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