Repositories list

• knox

  Public
  Full stack application for creating, combining, and storing combinatorial genetic design spaces.

  graph-algorithmssynthetic-biologycombinatorial-algorithms+ 1

  graph-algorithmssynthetic-biologycombinatorial-algorithmsgenetic-design

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •28•13•9•5•Updated Mar 5, 2026Mar 5, 2026

• Microfluidics-Benchmarks

  Public
  Consolidated Repo of Test Cases and Benchmarks

  Mint

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•2•Updated Mar 3, 2026Mar 3, 2026

• knoxAI

  Public

  CIDARLAB/knoxAI’s past year of commit activity
  A Machine Learning Microservice for Knox

  graph-algorithmssynthetic-biologyregression-algorithms+ 2

  graph-algorithmssynthetic-biologyregression-algorithmscombinatorial-algorithmsranking-algorithms

  Python

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated Feb 26, 2026Feb 26, 2026

• NeptuneGUI_2026

  Public

  CIDARLAB/NeptuneGUI_2026’s past year of commit activity
  GUI code for Neptune_2026

  Vue

  •1•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• pyparchmint

  Public
  pyparchmint is the defacto object library for describing microfluidic device architectures. It contains the base datastructures for provisioning physical layout…

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5•3•2•6•Updated Feb 10, 2026Feb 10, 2026

• pyLFR

  Public
  Python

  •3•3•12•3•Updated Feb 10, 2026Feb 10, 2026

• pyMINT

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•4•3•Updated Feb 10, 2026Feb 10, 2026

• DAFD

  Public

  CIDARLAB/DAFD’s past year of commit activity
  Python

  •7•17•0•14•Updated Feb 3, 2026Feb 3, 2026

• 3DuF

  Public
  Interactive microfluidic design editor

  microfluidicsfluigi

  microfluidicsfluigi

  JavaScript

  •

  BSD 2-Clause "Simplified" License

  •71•81•57•34•Updated Nov 22, 2025Nov 22, 2025

• pyFluigi

  Public

  CIDARLAB/pyFluigi’s past year of commit activity
  C++

  •5•0•1•1•Updated Nov 13, 2025Nov 13, 2025

• Oriole

  Public
  Verilog

  •2•0•0•0•Updated Mar 29, 2025Mar 29, 2025

• Vespa-Algorithm

  Public
  Python

  •1•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• Cello-v2-1-Core

  Public
  Streamlined Cello Algorithm. Feed it Verilog and UCF from CIDARLAB/CELLO-UCF, and run celloAlgo.py in terminal to make genetic circuit designs locally on your m…

  Python

  •

  Apache License 2.0

  •9•20•0•0•Updated Sep 16, 2024Sep 16, 2024

• constellation-js

  Public
  Library for combinatorially specifying, constraining, and exploring genetic design spaces.

  JavaScript

  •

  MIT License

  •8•1•0•1•Updated Aug 26, 2024Aug 26, 2024

• goldbar-generator

  Public
  Tool for GOLDBAR Generation using Rule Templates

  synthetic-biology

  synthetic-biology

  Python

  •0•1•0•0•Updated Aug 26, 2024Aug 26, 2024

• dafd-website

  Public
  Python

  •1•4•0•9•Updated Aug 6, 2024Aug 6, 2024

• pigeon

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •4•3•6•5•Updated Mar 23, 2024Mar 23, 2024

• mint-parchmint-scripts

  Public
  Python

  •0•0•0•0•Updated Nov 8, 2023Nov 8, 2023

• UCFormatter

  Public
  modify and visualize UCF files containing genetic part specifications

  Python

  •

  MIT License

  •1•2•0•0•Updated Jun 11, 2023Jun 11, 2023

• genetic-circuit-partitioning-new

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated May 28, 2023May 28, 2023

• pycello-v2

  Public
  Python classes for Cello v2 input and output formats, namely the netlist and the UCF.

  Python

  •1•0•0•1•Updated May 22, 2023May 22, 2023

• drop2image

  Public
  HTML

  •0•0•0•0•Updated May 11, 2023May 11, 2023

• Peripheral-Manager

  Public
  Talk to USB devices from the browser

  httpflaskmiddleware+ 3

  httpflaskmiddlewarehardwaresocket-iobridge

  Python

  •

  BSD 2-Clause "Simplified" License

  •2•3•1•2•Updated May 1, 2023May 1, 2023

• DAFD_Metrics

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 5, 2023Mar 5, 2023

• Neptune

  Public
  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •6•7•16•1•Updated Feb 19, 2023Feb 19, 2023

• neural-optimizer

  Public
  Python

  •2•3•0•8•Updated Feb 2, 2023Feb 2, 2023

• Cello-v2-webapp-gui

  Public
  This is the source for the GUI that supports the Cello v2 webapp. This repository exists only for development purposes. If you want to use the GUI, either visit…

  guisynthetic-biologywebapp+ 3

  guisynthetic-biologywebappcellogenetic-circuit-design-automationbio-design-automation

  JavaScript

  •3•1•5•19•Updated Jan 7, 2023Jan 7, 2023

• SS-Analyzer

  Public
  Python

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•3•Updated Dec 8, 2022Dec 8, 2022

• genetic-circuit-partitioning

  Public
  Partitioning a randomly sythesized graph, or

  Python

  •

  MIT License

  •0•1•0•0•Updated Nov 14, 2022Nov 14, 2022

• eugenecad

  Public
  The web site of the Eugene ecosystem

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•0•0•Updated Oct 26, 2022Oct 26, 2022