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 (kuznetsov@g.harvard.edu)

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

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

cd src/

git clone git@github.com:hsalis/Ribosome-Binding-Site-Calculator-v1.0.git rbs_calc

cd rbs_calc/

touch __init__.py

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
   

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

cd src/

./run_tests.sh

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.

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: otd@harvard.edu.

See the LICENSE file.