dnastack Documentation

This documentation describes how to install and run dnastack, a stochastic model of the the DNA stack chemistry described in paper: A Last-In First-Out Stack Data Structure Implemented in DNA, Lopiccolo and Shirt-Ediss, et al., Nature Comms 12, 4861 (2021) doi:10.1038/s41467-021-25023-6.

dnastack is written in Python 3 and makes use of the stocal simulation engine for polymer chemistries that have a variable size state space. The simulation outputs the predicted concentration of each DNA polymer species at the end of an experiment and these concentrations can be further displayed as virtual polyacrylamide gel images.

The source code for the model is available on Bitbucket, released under an MIT Licence.

Contents:

• Installation
  • Mac OS
  • Linux Ubuntu
  • Windows 10
• Quick Demo
• Running a Simulation
  • General Syntax
  • Defining a Gel
  • Specifying Washing Parameters
• Output Pickle File
  • Dictionary keys to general properties of the simulation
  • Dictionary keys to chemistry state at each simulation stage
• Virtual Gel Image