Pinned Repositories
bigg_models
The BiGG Models website server
cobradb
COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It already powers BiGG Models, and it is available under the MIT license.
cobrame
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
ecolime
Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression
lifelike
Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.
MASSpy
precise-db
A high-fidelity E. coli RNA-seq compendium
Protein_ML
Machine learning workflows for analyzing high-throughput protein data
Recon3D
A 3-Dimensional View of Human Metabolism and Disease
ssbio
A Python framework for structural systems biology
Systems Biology Research Group's Repositories
SBRG/MASSpy
SBRG/lifelike
Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.
SBRG/pymodulon
Python package for analyzing and visualizing iModulons
SBRG/GDGA_Shortcourse
Files for the Genome Design/Genome Analytics Short-course organized by the SBRG
SBRG/iModulonMiner
Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA
SBRG/MetPath
MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic models
SBRG/modulome_ppu
iModulon structure of Pseudomonas putida KT2440
SBRG/precise1k
SBRG/noncoding_alleleome
SBRG/precise2
SBRG/IM-ML
SBRG/modulytics
Visualization website for the modulome, a cross-species modularization of bacterial transcriptomes
SBRG/PromoterModeling
Sequence-based ML models of gene regulation
SBRG/pyphylon
Python package for analyzing and visualizing co-occuring gene / allele sets (phylons) within a pangenome
SBRG/RiboRid_Design
Design oligos for RiboRid protocol
SBRG/soplex_cython
Cython bindings to soplex 3.1.1
SBRG/Ecoli_chem_tol_ALE
SBRG/MASS-project
Template repository for a MASSpy project
SBRG/reference_sequences
Internal reference sequence bank
SBRG/ROS-ALE
Generates all figures for the manuscript "Laboratory evolution and advanced data analytics reveal systems biology of ROS tolerance" by Kevin Rychel, et al.
SBRG/dbgwas-network
SBRG/ElectricColi
Modeling and data analysis code for the E. coli extracellular electron transfer project
SBRG/GDS-Public
SBRG/lifelike-fix-modified-date
SBRG/lifelike-keycloak
Lifelike's custom Keycloak Docker image
SBRG/lifelike-website
Lifelike landing website
SBRG/ME-script
Notebooks for solving COBRAme models
SBRG/modulome_abaum
iModulon structure of Acinetobacter baumannii AB5075
SBRG/modulome_pst
iModulon structure of Pseudomonas syringae pv. tomato DC3000
SBRG/precise1k-analyze