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@DNA-and-Natural-Algorithms-Group DNA and Natural Algorithms Group

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    16 repositories

    • alhambra

      Public
      A package for designing and working with algorithmic DNA tile systems.
      Python
      •3•0•4•4•Updated Feb 28, 2026Feb 28, 2026

    • KinDA

      Public
      Kinetic DNA strand displacement analyzer
      Python
      •
      Other
      •6•17•0•1•Updated Oct 28, 2025Oct 28, 2025

    • multistrand

      Public
      Multistrand nucleic acid kinetic simulator
      C++
      •
      Other
      •11•21•0•1•Updated Oct 28, 2025Oct 28, 2025

    • stickydesign

      Public
      A package for designing short orthogonal and isoenergetic DNA sequences, intended for DNA tile sticky ends and often used for toeholds.
      Python
      •3•2•1•0•Updated Oct 30, 2024Oct 30, 2024

    • xgrow

      Public
      Simulator package for algorithmic tile self-assembly models aTAM and kTAM, as a python package.
      C
      •4•2•2•0•Updated May 8, 2024May 8, 2024

    • peppercompiler

      Public
      A compiler for DNA circuits and tile systems.
      Python
      •
      MIT License
      •3•3•0•1•Updated Dec 13, 2023Dec 13, 2023

    • piperine

      Public
      Piperine compiles abstract CRNs into DNA sequences and estimates how much the generated DNA implementations may participate in undesired DNA-DNA interactions du…
      Python
      •
      MIT License
      •6•22•1•1•Updated Dec 13, 2023Dec 13, 2023

    • SST-sequence-designer

      Public
      Sequence designer for single-stranded DNA tiles
      Python
      •
      Other
      •4•7•2•0•Updated Oct 26, 2023Oct 26, 2023

    • peppercornenumerator

      Public
      domain-level nucleic acid reaction enumeration
      Python
      •
      MIT License
      •6•10•0•0•Updated Aug 23, 2023Aug 23, 2023

    • nuskell

      Public
      Nucleic acid strand displacement compiler
      Python
      •
      MIT License
      •4•10•0•2•Updated Jul 25, 2023Jul 25, 2023

    • PathwayElaboration

      Public
      Predicitng nucleic acid kinetics with the pathway elaboration method
      Python
      •
      Other
      •0•2•0•0•Updated Feb 3, 2023Feb 3, 2023

    • surface_crns

      Public
      Package for simulating and displaying chemical reaction networks (CRNs) on a surface.
      Python
      •
      GNU General Public License v3.0
      •5•1•0•0•Updated Mar 19, 2021Mar 19, 2021

    • crnverifier

      Public
      Test the correctness of an implementation CRN, or the equivalence of two CRNs.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 11, 2021Jan 11, 2021

    • dsdobjects

      Public
      base classes for nucleic acid strand displacement programming
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 7, 2021Jan 7, 2021

    • FPEI

      Public
      Parameter estimation for interacting nucleic acid strands modelled as CTMCs, using a fixed path ensemble inference approach
      Python
      •
      Other
      •1•2•0•0•Updated Apr 26, 2020Apr 26, 2020

    • ArrheniusInference

      Public
      A framework with a reduced state space to train the Arrhenius DNA kinetic model
      Python
      •
      Other
      •5•6•0•0•Updated Oct 4, 2019Oct 4, 2019
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