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@UC-Davis-molecular-computing UC-Davis Molecular Computing Group

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    12 repositories

    • scadnano-python-package

      Public
      Python scripting library for generating designs readable by scadnano.
      dna-sequencescadnanodna-origami
      dna-sequencescadnanodna-origamidna-structures
      Python
      •
      MIT License
      •8•17•46•4•Updated Jul 13, 2026Jul 13, 2026

    • gpac

      Public
      package for numerically integrating differential equations (front-end for scipy.solve_ivp) using simpler syntax than scipy
      Jupyter Notebook
      •
      MIT License
      •0•2•3•0•Updated Jul 11, 2026Jul 11, 2026

    • batss

      Public
      BATching algorithm Stochastic Simulator for chemical reaction networks
      Jupyter Notebook
      •
      MIT License
      •1•1•11•0•Updated Jul 11, 2026Jul 11, 2026

    • nuad

      Public
      Nucleic acid sequence designer
      Jupyter Notebook
      •
      MIT License
      •8•12•44•4•Updated Jul 8, 2026Jul 8, 2026

    • scadnano

      Public
      Web application for designing DNA structures such as DNA origami.
      dna-sequencescadnanodna-origami
      dna-sequencescadnanodna-origamidna-structures
      Dart
      •
      MIT License
      •17•35•183•21•Updated Jun 28, 2026Jun 28, 2026

    • ode2tn

      Public
      Python package to compile an arbitrary polynomial ODE into a transcriptional network simulating it
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 26, 2026May 26, 2026

    • automata-solid

      Public
      automata simulator written in Typescript using SolidJS framework
      TypeScript
      •0•4•1•0•Updated Apr 6, 2026Apr 6, 2026

    • ppsim-rust

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•2•0•Updated Aug 5, 2025Aug 5, 2025

    • ppsim

      Public
      Python package for simulating population protocols
      Python
      •
      MIT License
      •5•10•19•0•Updated May 10, 2025May 10, 2025

    • labelator

      Public
      Python package for creating PDF documents that can be printed onto circular sticky labels that can be stuck to test tubes.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • simd-dna

      Public
      A Python simulator for the SIMD||DNA model of computation, as defined in the paper https://doi.org/10.1007/978-3-030-26807-7_12
      Python
      •
      MIT License
      •3•5•0•0•Updated Mar 11, 2023Mar 11, 2023

    • simd-dna-web-simulator

      Public
      A visual simulator for the SIMD||DNA model
      TypeScript
      •0•0•0•0•Updated May 31, 2022May 31, 2022
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