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rE.coli-57 software

Software library for recoding genomes used in Ostrov et al. (2016). Design, synthesis, and testing toward a 57-codon genome. Science, 353(6301).

Please contact us if you're interested in using this software for your own recoding projects: Gleb Kuznetsov ([email protected])

Setup

Setup python environment and install python dependencies

The software was developed and tested using python 2.7.

The required python libraries are listed in requirements.txt. We recommend using virtualenv to create a sandboxed environment.

virtualenv venv

source venv/bin/activate .

pip install -r requirements.txt

Install Unafold (required for secondary structure calculation).

  1. Download and install from here:

    http://homepages.rpi.edu/~zukerm/download/UNAFold_download.html

If using Linux, you probably want to download the RPM and use these instructions: https://overlappingminds.com/sh/thoughts/0aa6d79e-fb8b-4f84-b287-f8e4494eac49

Install Salis Ribosome Binding Site (RBS) Calculator

cd src/

git clone [email protected]:hsalis/Ribosome-Binding-Site-Calculator-v1.0.git rbs_calc

cd rbs_calc/

touch __init__.py

Install NUPACK (Nucleic Acid Package) - Required by Salis Calculator

  1. Download here http://www.nupack.org/. Our software expects Nupack to be located at /opt/nupack/. So either install it there, or update src/refactor_config.py.

  2. Copy the files in bin/ to /usr/local/bin

  3. Test that hybrid-ss-min can be run from the shell. Test the following command in a new terminal:

     hybrid-ss-min -h
    

Running tests

If using virtualenv, be sure the correct python environment is activated.

cd src/

./run_tests.sh

Usage

The main entry point to the code is src/main.py. After setting up the proper Python environment, you should be able to simply run:

cd src/

python main.py

Results are written to src/output.

License

Copyright (C) 2016 The President and Fellows of Harvard College

The Genome Recoder software is available under an internal non-commercial research and academic use license. Questions about this software or the licensing thereof can be addressed to Office of Technology Development, Harvard University, email: [email protected].

See the LICENSE file.

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Supporting code for Ostrov et al., Science, 2016

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