Explore @SBRG Open Source projects

Systems Biology Research Group (@SBRG)

SBRG

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420
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Registered over 11 years ago
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Python
43.6 %

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23.1 %

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10.3 %

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7.7 %

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2.6 %

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Objective-C
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GAP 2.6 %

Mathematica 2.6 %
Location 🇺🇸 United States
Country Total Rank 17,171
Country Ranking

GAP 47

Scheme
262

Mathematica 546

MATLAB
713

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ssbio

A Python framework for structural systems biology

bigg_models

The BiGG Models website server

cobrame

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

precise-db

A high-fidelity E. coli RNA-seq compendium

Jupyter Notebook

Recon3D

A 3-Dimensional View of Human Metabolism and Disease

Protein_ML

Machine learning workflows for analyzing high-throughput protein data

MASSpy

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.

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

Jupyter Notebook

GEMPro

Jupyter Notebook

iML1515_GP

GEM-PRO for the E. coli iML1515 metabolic model

minspan

ecolime

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

solvemepy

solveME public repository

MetPath

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

precise1k

Jupyter Notebook

ChIPdb

A Chromatin ImmunoPrecipitation database for PROkaryotic organisms.

modulome_ppu

iModulon structure of Pseudomonas putida KT2440

pcfba

Protein constrained FBA

Kinetome_profiling

precise2

sbaas

modulome_saci

iModulon structure of Sulfolobus acidocaldarius DSM 639

Jupyter Notebook

RibosomeProfiling

Analysis pipeline for characterization of microorganisms

oxidizeme

OxidizeME model and notebooks

ecoli_me_testing

Draft of the E. coli ME model to succeed iOL1650-ME

bop27refseq

bigg_models_data

The flat files for the BiGG Models website

modulytics

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

Strain_characterization_workflow

Code to characterize strains from multiple disparate data types

Jupyter Notebook

Bootcamp

MASS Toolbox Bootcamp

uFBA

unsteady-state Flux Balance Analysis (uFBA)

RiboRid_Design

Design oligos for RiboRid protocol

escher-maps

Extracted metabolic maps from simpheny/bigg1

IM-ML

Jupyter Notebook

MASS-Models

A collection of MASS Toolbox models

noncoding_alleleome

Jupyter Notebook

escher-fba

soplex_cython

Cython bindings to soplex 3.1.1

dynamicme

Dynamic ME simulations (separate module)

PromoterModeling

Sequence-based ML models of gene regulation

Jupyter Notebook