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    51 repositories

    • RetroTide

      Public
      PKS Retrobiosynthesis Tool
      Jupyter Notebook
      •
      Other
      •3•1•3•0•Updated Mar 26, 2026Mar 26, 2026

    • BioPKS-Pipeline

      Public
      Jupyter Notebook
      •
      Other
      •1•2•0•0•Updated Feb 25, 2026Feb 25, 2026

    • foldy-internal

      Public
      Internal foldy
      Jupyter Notebook
      •
      Other
      •1•0•0•1•Updated Feb 24, 2026Feb 24, 2026

    • media_compiler

      Public
      Code to create combinatorial media on the BioMek NXP platform with descriptions about how to use in an automated DBTL cycle.
      Jupyter Notebook
      •
      Other
      •0•3•0•0•Updated Feb 23, 2026Feb 23, 2026

    • DIVA

      Public
      A Design, Implementation, and Verification Automation Software Platform for DNA Construction
      Java
      •
      Other
      •0•1•0•0•Updated Feb 11, 2026Feb 11, 2026

    • ART

      Public
      A machine learning tool to improve the effectiveness of strain engineering in synthetic biology
      Jupyter Notebook
      •21•61•0•0•Updated Dec 15, 2025Dec 15, 2025

    • foldy

      Public
      Foldy: a web-based platform for interactive protein structure analysis
      TypeScript
      •
      Other
      •4•29•4•0•Updated Oct 28, 2025Oct 28, 2025

    • htp_16s

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • Isoprenol_CRISPRi

      Public
      Using data driving approaches with CRISPRi to improve isoprenol TRY
      Jupyter Notebook
      •
      Other
      •0•2•0•0•Updated Sep 22, 2025Sep 22, 2025

    • HamiltonVantage-Yeast_Transformation

      Public
      ReScript
      •
      Other
      •0•0•0•0•Updated Sep 9, 2025Sep 9, 2025

    • bayflux

      Public
      Software tool for Bayesian genome scale 13C Metabolic Flux Analysis
      Jupyter Notebook
      •
      Other
      •2•9•0•0•Updated Jun 26, 2025Jun 26, 2025

    • Flaviolin_media_opt_C3

      Public
      Data and notebooks for campaign 2 (C2) of media optimization for maximizing flaviolin yield in P. putida.
      Jupyter Notebook
      •
      Other
      •0•2•0•0•Updated Mar 27, 2025Mar 27, 2025

    • Flaviolin_media_opt_C2

      Public
      Data and notebooks for campaign 2 (C2) of media optimization for maximizing flaviolin titer in P. putida.
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Mar 27, 2025Mar 27, 2025

    • Flaviolin_media_opt_C1

      Public
      Media optimization for flaviolin producing P. putida
      Jupyter Notebook
      •
      Other
      •1•2•0•0•Updated Mar 27, 2025Mar 27, 2025

    • FluxRETAP

      Public
      Codebase for Flux REaction TArget Prioritization (Flux RETAP) code
      Jupyter Notebook
      •
      Other
      •0•3•0•0•Updated Jan 23, 2025Jan 23, 2025

    • edd

      Public
      Repository of standardized biological experimental data and metadata
      sciencesynbio
      sciencesynbio
      Python
      •
      Other
      •12•15•0•1•Updated Jan 9, 2025Jan 9, 2025

    • Repass_Kinetic_Model

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • BioParts

      Public
      Java
      •
      Other
      •0•0•0•0•Updated Jul 16, 2024Jul 16, 2024

    • ice

      Public
      Web based Registry platform for managing synthetic biological parts
      Java
      •
      Other
      •25•42•29•2•Updated May 16, 2024May 16, 2024

    • alphafold

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated May 14, 2024May 14, 2024

    • basebuddy

      Public
      A web app for recoding genes by organism.
      Jupyter Notebook
      •
      Other
      •8•6•0•0•Updated Feb 1, 2024Feb 1, 2024

    • ssgui

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Sep 28, 2023Sep 28, 2023

    • dnada

      Public
      DNAda is a web application that integrates the J5 DNA assembly software with robotic liquid handlers
      automationsynthetic-biologydna-assembly
      automationsynthetic-biologydna-assembly
      Python
      •
      Apache License 2.0
      •1•8•0•0•Updated Aug 28, 2023Aug 28, 2023

    • clusterCAD

      Public
      A computational platform for type I modular PKS and NRPS design
      Scheme
      •
      Other
      •7•13•1•7•Updated May 8, 2023May 8, 2023

    • DemoRepo

      Public template
      This repo is meant to demonstrate best practices with respect to code health and shareability.
      Jupyter Notebook
      •0•0•0•0•Updated Mar 30, 2023Mar 30, 2023

    • OMG

      Public
      Generate simulated -omics data for testing on Arrowland and EDD
      Jupyter Notebook
      •
      Other
      •3•3•1•4•Updated Dec 8, 2022Dec 8, 2022

    • edd-scripts

      Public
      Split out scripts not run by EDD from the main repository
      Python
      •0•0•0•2•Updated Dec 8, 2022Dec 8, 2022

    • edd-utils

      Public
      A set of utilities for working with Experiment Data Depot instances from python and the command line.
      Jupyter Notebook
      •
      Other
      •4•0•2•0•Updated Sep 15, 2022Sep 15, 2022

    • esm

      Public
      Evolutionary Scale Modeling (esm): Pretrained language models for proteins
      Python
      •
      MIT License
      •787•0•0•0•Updated Jul 20, 2022Jul 20, 2022

    • dash_escher

      Public
      A Plotly Dash component for EscherPy, a metabolic flux viewer.
      plotly-dash
      plotly-dash
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 12, 2022Jul 12, 2022
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