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@klavinslab Klavins Lab Software

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    55 repositories

    • klavinslab.github.io

      Public
      The Klavins Lab Web Page
      HTML
      •2•0•0•0•Updated Jun 19, 2025Jun 19, 2025

    • ipd_aq

      Public
      Institute for Protein Design's Instance of Aquarium
      Ruby
      •
      MIT License
      •0•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • aquaverse

      Public
      The Aquarium Portal
      HTML
      •
      MIT License
      •0•1•4•1•Updated Nov 16, 2023Nov 16, 2023

    • coral

      Public
      Coral, a library and framework for specifying synthetic biology design processes.
      Python
      •
      MIT License
      •8•33•1•2•Updated Dec 26, 2022Dec 26, 2022

    • moneyfish

      Public
      Get's transaction data from an Aquarium instance
      JavaScript
      •0•0•0•4•Updated Dec 9, 2022Dec 9, 2022

    • gofish

      Public
      Create a Node JS module from Aquarium's Javascript API
      JavaScript
      •0•0•0•3•Updated Dec 8, 2022Dec 8, 2022

    • slider

      Public
      Shows markdown files as slides for presentations.
      JavaScript
      •
      Other
      •0•0•0•8•Updated Dec 5, 2022Dec 5, 2022

    • enviro

      Public
      Multi-agent, multi-user environment
      C++
      •
      Other
      •12•3•3•2•Updated Dec 5, 2022Dec 5, 2022

    • crush

      Public
      Command line tools for developing Aquarium protocols
      JavaScript
      •1•1•0•0•Updated Apr 7, 2022Apr 7, 2022

    • biofab-nursery

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jul 8, 2021Jul 8, 2021

    • hp

      Public
      Hydrophobic-Polar 2D Protein Model
      Jupyter Notebook
      •0•0•0•0•Updated Jun 25, 2021Jun 25, 2021

    • tetra

      Public archive
      TETRA: Time Estimation Tool For Aquarium
      Ruby
      •0•0•0•0•Updated Jun 16, 2021Jun 16, 2021

    • gro

      Public
      The gro bacterial micro-colony growth specification and simulation software. For more information see the gro website, listed below.
      Mathematica
      •
      Other
      •17•52•1•0•Updated Feb 16, 2021Feb 16, 2021

    • Aquarium-High-Throughput-Culturing

      Public
      Aquarium High Throughput Culturing: An Aquarium Workflow
      HTML
      •
      Other
      •1•1•0•1•Updated Aug 6, 2020Aug 6, 2020

    • Jellyfish

      Public
      Scripts for accessing information about Aquarium High Throughput Culturing operation types through Trident API.
      Jupyter Notebook
      •
      Other
      •3•1•1•1•Updated Jul 15, 2020Jul 15, 2020

    • ngs-review

      Public
      Protocols for NGS
      HTML
      •
      Other
      •0•0•0•1•Updated May 29, 2020May 29, 2020

    • aq-graphics

      Public
      Aquarium SVG Graphics Library: An Aquarium Library
      HTML
      •
      Other
      •0•0•4•0•Updated May 28, 2020May 28, 2020

    • OLA-Simple

      Public
      OLA Simple HIV Drug Resistance Test: An Aquarium Workflow
      HTML
      •0•0•0•0•Updated May 13, 2020May 13, 2020

    • BIOFAB_Production

      Public
      A copy of the BIOFAB production protocols.
      Ruby
      •0•0•0•0•Updated May 12, 2020May 12, 2020

    • ProtocolsForReview

      Public
      Current (as of April 20) protocols for review
      Ruby
      •0•0•0•0•Updated Apr 20, 2020Apr 20, 2020

    • library-protocol-dependencies

      Public
      Python
      •0•0•0•0•Updated Mar 9, 2020Mar 9, 2020

    • elma

      Public
      An event loop manager for reactive, embedded systems
      C++
      •
      Other
      •23•9•1•1•Updated Mar 9, 2020Mar 9, 2020

    • elma_project

      Public
      An example project that uses the Elma reactive systems library
      C++
      •
      Other
      •12•2•0•0•Updated Feb 4, 2020Feb 4, 2020

    • flow-cytometry

      Public
      Flow Cytometry: An Aquarium Workflow
      HTML
      •
      Other
      •0•0•0•0•Updated Jan 16, 2020Jan 16, 2020

    • media-workflow

      Public
      Liquid/Agar Media Workflow: An Aquarium Workflow
      HTML
      •
      Other
      •0•0•0•0•Updated Dec 4, 2019Dec 4, 2019

    • aquarium-bugs

      Public
      A repo formerly for reporting bugs and feature requests related to the Aquarium software.
      2•2•166•0•Updated Nov 14, 2019Nov 14, 2019

    • ssb-book

      Public
      Systems and Synthetic Biology Book
      Mathematica
      •2•3•0•0•Updated Apr 10, 2019Apr 10, 2019

    • test-workflow

      Public
      Workflow test-workflow published from Aquarium
      HTML
      •
      Other
      •0•0•0•0•Updated Apr 1, 2019Apr 1, 2019

    • simple-plasmid-construction

      Public
      UW BIOFAB Simple Plasmid Construction: An Aquarium Workflow
      HTML
      •
      Other
      •0•1•0•0•Updated Apr 1, 2019Apr 1, 2019

    • primer-workflow

      Public
      Primer Workflow: An Aquarium Workflow
      HTML
      •
      Other
      •0•0•2•0•Updated Apr 1, 2019Apr 1, 2019