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    44 repositories

    • RetroTide

      Public
      PKS Retrobiosynthesis Tool
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • BiosynthPipeline

      Public
      Hybrid retrobiosynthesis pipeline for biosynthetic pathway design
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • edd

      Public
      Repository of standardized biological experimental data and metadata
      sciencesynbio
      Python
      •
      Other
      •12•14•0•1•Updated Oct 3, 2024Oct 3, 2024

    • 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•0•0•0•Updated Aug 27, 2024Aug 27, 2024

    • 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•0•0•0•Updated Aug 27, 2024Aug 27, 2024

    • 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•1•0•0•Updated Aug 17, 2024Aug 17, 2024

    • Flaviolin_media_opt_C1

      Public
      Media optimization for flaviolin producing P. putida
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Aug 17, 2024Aug 17, 2024

    • BioParts

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

    • bayflux

      Public
      Software tool for Bayesian genome scale 13C Metabolic Flux Analysis
      Jupyter Notebook
      •
      Other
      •2•4•0•0•Updated Jul 12, 2024Jul 12, 2024

    • ice

      Public
      Web based Registry platform for managing synthetic biological parts
      Java
      •
      Other
      •24•40•28•2•Updated May 16, 2024May 16, 2024

    • alphafold

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

    • foldy

      Public
      Foldy: a web-based platform for interactive protein structure analysis
      TypeScript
      •
      Other
      •2•21•13•0•Updated Apr 11, 2024Apr 11, 2024

    • basebuddy

      Public
      A web app for recoding genes by organism.
      Jupyter Notebook
      •
      Other
      •6•4•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
      Python
      •
      Apache License 2.0
      •1•8•0•0•Updated Aug 28, 2023Aug 28, 2023

    • ART

      Public
      A machine learning tool to improve the effectiveness of strain engineering in synthetic biology
      Jupyter Notebook
      •20•54•1•0•Updated Aug 22, 2023Aug 22, 2023

    • clusterCAD

      Public
      A computational platform for type I modular PKS and NRPS design
      Scheme
      •
      Other
      •6•11•0•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•0•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
      •638•0•0•0•Updated Jul 20, 2022Jul 20, 2022

    • dash_escher

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

    • Omics-Data-QA-QC-tool

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Jun 23, 2022Jun 23, 2022

    • library_loading_concentration_prediction

      Public
      A tool to predict library loading concentration from cluster density and bioanalyzer data.
      machine-learningsequencing
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•5•3•Updated Jun 22, 2022Jun 22, 2022

    • KineticLearning

      Public
      Learning Kinetic Models from Time Series Proteomics and Metabolomics Data
      machine-learningsynbiokinetic-modeling
      Jupyter Notebook
      •
      Other
      •17•28•0•2•Updated Jun 21, 2022Jun 21, 2022

    • vectoreditor

      Public
      Web based DNA sequence editing and analysis tool
      ActionScript
      •8•14•4•0•Updated Sep 27, 2021Sep 27, 2021

    • wors

      Public
      CSS
      •
      Other
      •0•0•0•0•Updated Jun 28, 2021Jun 28, 2021

    • acor

      Public
      Estimate the autocorrelation time of time-series data very quickly
      C
      •
      MIT License
      •18•0•0•0•Updated Aug 13, 2020Aug 13, 2020

    • jqmm

      Public
      JBEI Quantitative Metabolic Modeling library
      Jupyter Notebook
      •
      Other
      •10•12•0•1•Updated Feb 7, 2020Feb 7, 2020