Multistrand

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Overview

What is Multistrand?

Multistrand is a software package for simulating the kinetics of multiple interacting nucleic acid strands. It is developed at the Winfree lab at the California Institute of Technology.

DNA and Natural Algorithms Group @ Caltech

Multistrand statespace

Key Features

  • Kinetic simulations of nucleic acids as random walk on thermodynamic energy model
  • Supports multiple interacting strands
  • Equilibrium consistent with NUPACK
  • Various usage modes to study kinetic trajectories
  • Distributed as a Python package
  • MIT License
  We want your feedback!
Bug reports, success stories, help inquiries, feature requests... send them to help@multistrand.org

  If you use Multistrand in your research please cite one or more of the following:
Joseph M. Schaeffer (2013) Stochastic simulation of the kinetics of multiple interacting nucleic acid strands. Dissertation (Ph.D.), California Institute of Technology.
Joseph M. Schaeffer, Chris Thachuk, Erik Winfree (2015) Stochastic simulation of the kinetics of multiple interacting nucleic acid strands. DNA Computing and Molecular Programming (DNA21), Lecture Notes in Computer Science (LNCS) volume 9211, pp 194-211.
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Installation

Getting Multistrand

  • Option 1: Use online version

    The KinDA project bundles Multistrand along with other useful software into a Public AWS Image. Using that predefined machine image in the Amazon cloud ensures you can get started with Multistrand right away, with all of the necessary dependencies already installed.

    Go to KinDA project site

  • Option 2: Install from source

    For longer simulations and better integration with your analysis pipeline, Multistrand can also be installed locally on your system.

    Detailed installation instructions can be found in the README file.

    Version 2.1

    Multistrand is hosted on github:

    Visit our github page

    Download Multistrand 2.1 as .zip:

    Download .zip
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Tutorials

How to use Multistrand

  Interactive versions of these tutorials are available.

  1. Hairpin Energies.
    See how to make a complex, calculate its energy, and plot a simple energy landscape for hairpin folding.
  2. Hairpin Trajectories.
    See how to set up a simulation, and how to recover the states visited.
  3. Hairpin Transitions.
    See how to define macrostates, so that the simulation doesn't return every elementary step, but just returns when a macrostate is entered or exited. See how to abulate transition frequencies between macrostates, and examine the consequences of using loose macrostates.
  4. Hairpin First Passage Time.
    Don't look at trajectories, just tabulate how long they took, and compute statistics. See the effects of kinetic traps in folding, and use the random number seed to reproduce trajectories of interest.
  5. Three-way Branch Migration Energies.
    See how to define complexes with multiple strands. Consider the energy of a test tube. Plot test tube energy for a hypothetical pathway for toehold-mediated three-way strand displacement.
  6. Three-way Branch Migration Trajectories.
    Run simulations in which strands might dissociate. Look at how to extract information from the trajectories.
  7. Three-way Branch Migration Transitions.
    Transition mode for multistranded systems. Again, compare exact versus loose macrostates.
  8. Three-way Branch Migration First Passage Time.
    Compare two sequence designs based on (a) their duration statistics, and (b) their frequencies of reaching either "success" or "failure" states.
  9. (coming soon) Hybridization First Step Mode.
    Preferred method for deducing bimolecular rate constants. Details on more efficient simulation that skips "equilibration" between interactions. Deduce first-order and second-order rate constants from probability of success and time to completion, with error bars!
  10. (coming soon) Hybridization Comparison.
    Look at two strands interacting in a tiny box. Compare sequences that are unstructured vs have hairpins in various locations. Compute association and dissociation rate constants. Compare using first passage time, transition mode, and first step mode. See how the time to reach a full duplex scales with concentration.
  11. (coming soon) Threeway Branch Migration First Step Mode.
    Automate the running of a month's worth of simulations to examine the dependence of toehold-mediated strand displacement rate constants on toehold length.
  12. NUPACK calls.
    Explore how to call various NUPACK functions using the NUPACK python wrapper distributed with Multistrand.
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Contact

help@multistrand.org
DNA and Natural Algorithms Group @ Caltech