Systems Biology Research Group

MASSpy

lifelike

Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.

pymodulon

Python package for analyzing and visualizing iModulons

GDGA_Shortcourse

Files for the Genome Design/Genome Analytics Short-course organized by the SBRG

ChIPdb

A Chromatin ImmunoPrecipitation database for PROkaryotic organisms.

MetPath

MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic models

modulome_ppu

iModulon structure of Pseudomonas putida KT2440

precise1k

modulome_saci

iModulon structure of Sulfolobus acidocaldarius DSM 639

precise2

IM-ML

iModulonMiner

Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA

modulytics

Visualization website for the modulome, a cross-species modularization of bacterial transcriptomes

noncoding_alleleome

RiboRid_Design

Design oligos for RiboRid protocol

soplex_cython

Cython bindings to soplex 3.1.1

MASS-project

Template repository for a MASSpy project

MASSdb

Source code for the MASS database project.

dbgwas-network

Ecoli_chem_tol_ALE

GDS-Public

lifelike-fix-modified-date

lifelike-keycloak

Lifelike's custom Keycloak Docker image

lifelike-website

Lifelike landing website

ME-script

Notebooks for solving COBRAme models

modulome_abaum

iModulon structure of Acinetobacter baumannii AB5075

modulome_pst

iModulon structure of Pseudomonas syringae pv. tomato DC3000

precise1k-analyze

reference_sequences

Internal reference sequence bank

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.