Pinned Repositories
ART
A machine learning tool to improve the effectiveness of strain engineering in synthetic biology
clusterCAD
A computational platform for type I modular PKS and NRPS design
dnada
DNAda is a web application that integrates the J5 DNA assembly software with robotic liquid handlers
edd
Repository of standardized biological experimental data and metadata
foldy
Foldy: a web-based platform for interactive protein structure analysis
ice
Web based Registry platform for managing synthetic biological parts
jqmm
JBEI Quantitative Metabolic Modeling library
KineticLearning
Learning Kinetic Models from Time Series Proteomics and Metabolomics Data
prpr
vectoreditor
Web based DNA sequence editing and analysis tool
Joint BioEnergy Institute's Repositories
JBEI/ART
A machine learning tool to improve the effectiveness of strain engineering in synthetic biology
JBEI/ice
Web based Registry platform for managing synthetic biological parts
JBEI/KineticLearning
Learning Kinetic Models from Time Series Proteomics and Metabolomics Data
JBEI/foldy
Foldy: a web-based platform for interactive protein structure analysis
JBEI/edd
Repository of standardized biological experimental data and metadata
JBEI/vectoreditor
Web based DNA sequence editing and analysis tool
JBEI/clusterCAD
A computational platform for type I modular PKS and NRPS design
JBEI/jqmm
JBEI Quantitative Metabolic Modeling library
JBEI/dnada
DNAda is a web application that integrates the J5 DNA assembly software with robotic liquid handlers
JBEI/basebuddy
A web app for recoding genes by organism.
JBEI/bayflux
Software tool for Bayesian genome scale 13C Metabolic Flux Analysis
JBEI/OMG
Generate simulated -omics data for testing on Arrowland and EDD
JBEI/biosensor_characterization_public
Code for MCMC Analysis of Transcription Factor Based Biosensors
JBEI/library_loading_concentration_prediction
A tool to predict library loading concentration from cluster density and bioanalyzer data.
JBEI/BioParts
JBEI/DemoRepo
This repo is meant to demonstrate best practices with respect to code health and shareability.
JBEI/edd-utils
A set of utilities for working with Experiment Data Depot instances from python and the command line.
JBEI/acor
Estimate the autocorrelation time of time-series data very quickly
JBEI/Ajinomoto
Ajinomoto Project Data Analysis
JBEI/alphafold
JBEI/dash_escher
A Plotly Dash component for EscherPy, a metabolic flux viewer.
JBEI/edd-scripts
Split out scripts not run by EDD from the main repository
JBEI/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
JBEI/Flaviolin_media_opt_C1
Media optimization for flaviolin producing P. putida
JBEI/Flaviolin_media_opt_C2
Data and notebooks for campaign 2 (C2) of media optimization for maximizing flaviolin titer in P. putida.
JBEI/Flaviolin_media_opt_C3
Data and notebooks for campaign 2 (C2) of media optimization for maximizing flaviolin yield in P. putida.
JBEI/media_compiler
Code to create combinatorial media on the BioMek NXP platform with descriptions about how to use in an automated DBTL cycle.
JBEI/Omics-Data-QA-QC-tool
JBEI/ssgui
JBEI/wors