scadnano 0.8.0

Python scripting library for generating designs readable by scadnano.

scadnano-python-package

The scadnano Python module is a library for describing synthetic DNA nanostructures (e.g., DNA origami).

If you find scadnano useful in a scientific project, please cite its associated paper:

scadnano: A browser-based, easily scriptable tool for designing DNA nanostructures.
David Doty, Benjamin L Lee, and Tristan Stérin.
Technical Report 2005.11841, arXiv, 2020.
[ arXiv paper | BibTeX ]

Overview

This module is used to write Python scripts outputting .dna files readable by scadnano, a web application useful for displaying and manually editing these structures. The purpose of this module is to help automate some of the task of creating DNA designs, as well as making large-scale changes to them that are easier to describe programmatically than to do by hand in scadnano.

Reporting issues

Please report issues in the web interface at the scadnano web interface GitHub repository, and report issues in the Python scripting library at the scadnano Python package GitHub repository.

Installation

The scadnano Python package requires Python version 3.7 or later. If you do not have that version (or later) of Python installed, follow this link to install it.

Once Python is installed, there are two ways you can install the scadnano Python package:

1. pip

   Use pip to install the package by executing the following at the command line:

   pip install scadnano
   

   If your Python installation does not already have pip installed, you may have to install it. Executing this Python script should work; see also https://docs.python.org/3/installing/index.html or https://www.liquidweb.com/kb/install-pip-windows/.

2. download

   As a simple alternative, you can download and place the following files (located in the scadnano/ subfolder) in your PYTHONPATH (e.g., in the same directory as the scripts you are running):

   • required: scadnano.py
   • required: scadnano_version.py
   • optional: modifications.py; This contains some common DNA modifications such as biotin and Cy3.
   • optional: origami_rectangle.py; This can help create origami rectangles, but it is not necessary to use scadnano.

   Unfortunately, the scadnano package depends on the Python package xlwt, so xlwt must be installed. To install, type pip install xlwt at the command line. If this does not work, then you can comment out the line import xlwt in scadnano.py, but then you will not be able to call the method DNADesign.write_idt_plate_excel_file() to export an Excel file with DNA sequences.

Documentation

Online documentation of the package API is located here: https://scadnano-python-package.readthedocs.io

Tutorial

A tutorial shows how to create a "standard" 24-helix DNA origami rectangle using the scripting library.

Examples

Several example scripts are located in the examples/ subfolder. Their output is contained in the examples/output_designs/ subfolder.