DNA and Natural Algorithms Group

DNA and Natural Algorithms Group's repositories

piperine

Piperine compiles abstract CRNs into DNA sequences and estimates how much the generated DNA implementations may participate in undesired DNA-DNA interactions during experiments.

Language:PythonMIT22 5 2

multistrand

Multistrand nucleic acid kinetic simulator

Language:C++17 7 5

peppercornenumerator

domain-level nucleic acid reaction enumeration

Language:PythonMIT10 40

KinDA

Kinetic DNA strand displacement analyzer

Language:PythonNOASSERTION8 50

nuskell

Nucleic acid strand displacement compiler

Language:PythonMIT800

SST-sequence-designer

Sequence designer for single-stranded DNA tiles

Language:PythonNOASSERTION600

ArrheniusInference

A framework with a reduced state space to train the Arrhenius DNA kinetic model

Language:PythonNOASSERTION4 50

peppercompiler

A compiler for DNA circuits and tile systems.

Language:PythonMIT3 3 1

xgrow

Simulator package for algorithmic tile self-assembly models aTAM and kTAM, as a python package.

Language:C300

FPEI

Parameter estimation for interacting nucleic acid strands modelled as CTMCs, using a fixed path ensemble inference approach

Language:PythonNOASSERTION200

PathwayElaboration

Predicitng nucleic acid kinetics with the pathway elaboration method

Language:PythonNOASSERTION200

stickydesign

A package for designing short orthogonal and isoenergetic DNA sequences, intended for DNA tile sticky ends and often used for toeholds.

Language:Python200

surface_crns

Package for simulating and displaying chemical reaction networks (CRNs) on a surface.

Language:PythonGPL-3.0100

alhambra

A package for designing and working with algorithmic DNA tile systems.

Language:Python000

crnverifier

Test the correctness of an implementation CRN, or the equivalence of two CRNs.

Language:PythonMIT000

dsdobjects

base classes for nucleic acid strand displacement programming

Language:PythonMIT000