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ssbio
A Python framework for structural systems biologycobrame
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)precise-db
A high-fidelity E. coli RNA-seq compendiumRecon3D
A 3-Dimensional View of Human Metabolism and DiseaseProtein_ML
Machine learning workflows for analyzing high-throughput protein dataMASSpy
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 iModulonsGDGA_Shortcourse
Files for the Genome Design/Genome Analytics Short-course organized by the SBRGGEMPro
iML1515_GP
GEM-PRO for the E. coli iML1515 metabolic modelminspan
ecolime
Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expressionsolvemepy
solveME public repositoryMetPath
MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic modelsprecise1k
ChIPdb
A Chromatin ImmunoPrecipitation database for PROkaryotic organisms.modulome_ppu
iModulon structure of Pseudomonas putida KT2440pcfba
Protein constrained FBAKinetome_profiling
precise2
sbaas
modulome_saci
iModulon structure of Sulfolobus acidocaldarius DSM 639RibosomeProfiling
Analysis pipeline for characterization of microorganismsoxidizeme
OxidizeME model and notebooksecoli_me_testing
Draft of the E. coli ME model to succeed iOL1650-MEbop27refseq
bigg_models_data
The flat files for the BiGG Models websitemodulytics
Visualization website for the modulome, a cross-species modularization of bacterial transcriptomesStrain_characterization_workflow
Code to characterize strains from multiple disparate data typesBootcamp
MASS Toolbox BootcampuFBA
unsteady-state Flux Balance Analysis (uFBA)RiboRid_Design
Design oligos for RiboRid protocolescher-maps
Extracted metabolic maps from simpheny/bigg1IM-ML
MASS-Models
A collection of MASS Toolbox modelsnoncoding_alleleome
escher-fba
soplex_cython
Cython bindings to soplex 3.1.1dynamicme
Dynamic ME simulations (separate module)PromoterModeling
Sequence-based ML models of gene regulationLove Open Source and this site? Check out how you can help us