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    • RetroTide

      Public
      PKS Retrobiosynthesis Tool
      Jupyter Notebook
      Other
      3130Updated Mar 26, 2026Mar 26, 2026
    • Jupyter Notebook
      Other
      1200Updated Feb 25, 2026Feb 25, 2026
    • Internal foldy
      Jupyter Notebook
      Other
      1001Updated Feb 24, 2026Feb 24, 2026
    • Code to create combinatorial media on the BioMek NXP platform with descriptions about how to use in an automated DBTL cycle.
      Jupyter Notebook
      Other
      0300Updated Feb 23, 2026Feb 23, 2026
    • DIVA

      Public
      A Design, Implementation, and Verification Automation Software Platform for DNA Construction
      Java
      Other
      0100Updated Feb 11, 2026Feb 11, 2026
    • ART

      Public
      A machine learning tool to improve the effectiveness of strain engineering in synthetic biology
      Jupyter Notebook
      216100Updated Dec 15, 2025Dec 15, 2025
    • foldy

      Public
      Foldy: a web-based platform for interactive protein structure analysis
      TypeScript
      Other
      42940Updated Oct 28, 2025Oct 28, 2025
    • htp_16s

      Public
      Python
      Other
      0000Updated Oct 16, 2025Oct 16, 2025
    • Using data driving approaches with CRISPRi to improve isoprenol TRY
      Jupyter Notebook
      Other
      0200Updated Sep 22, 2025Sep 22, 2025
    • ReScript
      Other
      0000Updated Sep 9, 2025Sep 9, 2025
    • bayflux

      Public
      Software tool for Bayesian genome scale 13C Metabolic Flux Analysis
      Jupyter Notebook
      Other
      2900Updated Jun 26, 2025Jun 26, 2025
    • Data and notebooks for campaign 2 (C2) of media optimization for maximizing flaviolin yield in P. putida.
      Jupyter Notebook
      Other
      0200Updated Mar 27, 2025Mar 27, 2025
    • Data and notebooks for campaign 2 (C2) of media optimization for maximizing flaviolin titer in P. putida.
      Jupyter Notebook
      Other
      0100Updated Mar 27, 2025Mar 27, 2025
    • Media optimization for flaviolin producing P. putida
      Jupyter Notebook
      Other
      1200Updated Mar 27, 2025Mar 27, 2025
    • FluxRETAP

      Public
      Codebase for Flux REaction TArget Prioritization (Flux RETAP) code
      Jupyter Notebook
      Other
      0300Updated Jan 23, 2025Jan 23, 2025
    • edd

      Public
      Repository of standardized biological experimental data and metadata
      Python
      Other
      121501Updated Jan 9, 2025Jan 9, 2025
    • Jupyter Notebook
      0000Updated Sep 4, 2024Sep 4, 2024
    • BioParts

      Public
      Java
      Other
      0000Updated Jul 16, 2024Jul 16, 2024
    • ice

      Public
      Web based Registry platform for managing synthetic biological parts
      Java
      Other
      2542292Updated May 16, 2024May 16, 2024
    • alphafold

      Public
      Python
      Apache License 2.0
      0000Updated May 14, 2024May 14, 2024
    • basebuddy

      Public
      A web app for recoding genes by organism.
      Jupyter Notebook
      Other
      8600Updated Feb 1, 2024Feb 1, 2024
    • ssgui

      Public
      Python
      Other
      0000Updated Sep 28, 2023Sep 28, 2023
    • dnada

      Public
      DNAda is a web application that integrates the J5 DNA assembly software with robotic liquid handlers
      Python
      Apache License 2.0
      1800Updated Aug 28, 2023Aug 28, 2023
    • A computational platform for type I modular PKS and NRPS design
      Scheme
      Other
      71317Updated 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
      0000Updated Mar 30, 2023Mar 30, 2023
    • OMG

      Public
      Generate simulated -omics data for testing on Arrowland and EDD
      Jupyter Notebook
      Other
      3314Updated Dec 8, 2022Dec 8, 2022
    • Split out scripts not run by EDD from the main repository
      Python
      0002Updated 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
      4020Updated Sep 15, 2022Sep 15, 2022
    • esm

      Public
      Evolutionary Scale Modeling (esm): Pretrained language models for proteins
      Python
      MIT License
      787000Updated Jul 20, 2022Jul 20, 2022
    • A Plotly Dash component for EscherPy, a metabolic flux viewer.
      Python
      MIT License
      0000Updated Jul 12, 2022Jul 12, 2022
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