Coral, a library and framework for specifying synthetic biology design processes.
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README.md

coral

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Documentation Status

Coral: Core tools for synthetic DNA design. Read the documentation at http://coral.readthedocs.org.

Coral is a Python library for encoding the process of designing synthetic DNA constructs. Coral mirrors the traditional design steps used in GUI-based sequence design (ApE, j5, Benchling, etc.) as operations on data structures, enables iterative design through analysis modules, and connects seamlessly to outside libraries. Through the use of Coral, you can translate your DNA design processes into concise, executable, and reusable scripts.

Coral encodes synthetic DNA design rules into its core sequence data types (DNA, RNA, and Peptide), enabling concise, dependable methods for automated DNA design.

Coral works with PyPy so long as a PyPy-compatible numpy is installed.

Installation:

Most users:

pip install coral

Windows users:

Install vcpython2.7 (http://aka.ms/vcpython27) if it's not already installed, then

pip install coral

Many Windows users have a better time installing python packages, including coral, using Anaconda.

To get the latest on git:

git clone https://github.com/klavinslab/coral.git
cd coral
pip install .

Docker images available here: https://hub.docker.com/u/coraldesign/

Requirements:

###python (pip-compatible):

numpy
biopython

optional:

Package Added functionality
matplotlib plotting sequencing analysis
intermine, requests yeast database (intermine) functions

###system:

Package Added functionality
NuPack Structural analysis
ViennaRNA Structural analysis

Development:

Install the extra packages in dev-requirements.txt (Sphinx, cython, nose).

License

MIT

Author

The author and maintainer of Coral is Nick Bolten. Contact him (me) at nbolten@gmail.com with any and all Coral questions (don't be shy!).

Changelog

View the changelog here.