Systems Biology Research Group

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cobradb cobradb Public

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.

Python 20 11
ssbio ssbio Public

A Python framework for structural systems biology

Python 102 28
cobrame cobrame Public

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Python 33 17
ecolime ecolime Public

Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

Python 4 12
bigg_models bigg_models Public

The BiGG Models website server

Python 75 18
precise-db precise-db Public

A high-fidelity E. coli RNA-seq compendium

Jupyter Notebook 32 19

Repositories

iModulonMiner Public Forked from avsastry/modulome-workflow
Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA

SBRG/iModulonMiner’s past year of commit activity

HTML 2 MIT 19 3 1 Updated Jul 15, 2024
pymodulon Public
Python package for analyzing and visualizing iModulons

SBRG/pymodulon’s past year of commit activity

Python 9 MIT 11 8 (2 issues need help) 3 Updated Jul 2, 2024
ElectricColi Public
Modeling and data analysis code for the E. coli extracellular electron transfer project

SBRG/ElectricColi’s past year of commit activity

Jupyter Notebook 0 MIT 0 0 0 Updated Jun 29, 2024
pyphylon Public
Python package for analyzing and visualizing co-occuring gene / allele sets (phylons) within a pangenome

SBRG/pyphylon’s past year of commit activity

Python 1 MIT 0 3 0 Updated Jun 17, 2024
GDS-Public Public

SBRG/GDS-Public’s past year of commit activity

Jupyter Notebook 0 MIT 0 0 0 Updated May 8, 2024
noncoding_alleleome Public

SBRG/noncoding_alleleome’s past year of commit activity

Jupyter Notebook 1 MIT 0 0 0 Updated Apr 16, 2024
lifelike Public archive
Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.

SBRG/lifelike’s past year of commit activity

Python 20 4 0 28 Updated Apr 4, 2024
MetPath Public
MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic models

SBRG/MetPath’s past year of commit activity

MATLAB 3 MIT 1 0 0 Updated Oct 19, 2023
precise1k-analyze Public

SBRG/precise1k-analyze’s past year of commit activity

Jupyter Notebook 0 MIT 0 0 0 Updated Oct 10, 2023
modulytics Public
Visualization website for the modulome, a cross-species modularization of bacterial transcriptomes

SBRG/modulytics’s past year of commit activity

1 MIT 3 2 1 Updated Sep 16, 2023