Systems Biology Research Group

Repositories

• pymodulon

  Python package for analyzing and visualizing iModulons
  Python MIT 1 4 7 (1 issue needs help) 1 Updated Jul 19, 2021

• ChIPdb

  A Chromatin ImmunoPrecipitation database for PROkaryotic organisms.
  Jupyter Notebook MIT 0 2 0 0 Updated Jul 16, 2021

• modulytics

  Visualization website for the modulome, a cross-species modularization of bacterial transcriptomes
  MIT 0 0 0 0 Updated Jul 10, 2021

• precise2
  Jupyter Notebook 0 0 0 0 Updated Jun 13, 2021

• oxidizeme

  OxidizeME model and notebooks
  Python 3 2 0 2 Updated Jun 11, 2021

• solvemepy

  solveME public repository
  Python MIT 5 2 3 1 Updated Jun 11, 2021

• MASSpy
  Python MIT 2 9 3 0 Updated May 9, 2021

• precise-db

  A high-fidelity E. coli RNA-seq compendium
  Jupyter Notebook MIT 13 19 1 0 Updated Mar 5, 2021

• reference_sequences

  Internal reference sequence bank
  2 0 0 1 Updated Jan 25, 2021

• MASSpy-ExampleProject

  A template repository providing an example of how to structure a MASSpy project.
  Python MIT 0 0 0 0 Updated Jan 20, 2021

• svns_refseq
  0 0 0 0 Updated Dec 18, 2020

• ssbio

  A Python framework for structural systems biology

  structural-biology protein-structure systems-biology cobrapy constraint-based-modeling structural-systems-biology
  Python MIT 16 63 23 1 Updated Dec 7, 2020

• xplatform_ica_paper

  Data and code for "Matrix factorization recovers consistent regulatory signals from disparate datasets"
  Jupyter Notebook MIT 0 0 0 0 Updated Nov 18, 2020

• bitome

  Analysis of binarized genome-scale feature information for E. coli K-12 MG1655
  Jupyter Notebook MIT 0 0 0 0 Updated Nov 12, 2020

• MASSpy-publication

  Scripts and notebooks needed to reproduce case studies in MASSpy publication.
  Jupyter Notebook MIT 0 0 0 0 Updated Oct 27, 2020

• MinIONtoModels
  0 0 0 0 Updated Oct 15, 2020

• modulome_compare_data

  Repository of bbh data for organisms in Modulome
  0 0 0 0 Updated Sep 2, 2020

• Kinetome_profiling
  R 2 2 0 0 Updated Aug 7, 2020

• bop27refseq
  HTML 1 1 0 0 Updated Dec 22, 2019

• bigg_models

  The BiGG Models website server
  Python 14 53 81 0 Updated Nov 7, 2019

• bigg_models_data

  The flat files for the BiGG Models website
  Python 3 1 0 0 Updated Oct 30, 2019

• 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.

  python sqlalchemy database
  Python 9 16 2 0 Updated Oct 29, 2019

• iML1515_GP

  GEM-PRO for the E. coli iML1515 metabolic model
  Scheme 2 1 0 0 Updated Oct 17, 2019

• MetPath

  MetPath is a set of functions for performing metabolic pathway-based gene expression analysis using genome-scale metabolic models
  MATLAB MIT 1 1 0 0 Updated Oct 3, 2019

• global-maps-internship-scripts
  Python MIT 1 0 25 0 Updated Jul 29, 2019

• escher-fba
  JavaScript MIT 0 0 0 0 Updated Jul 15, 2019

• ecolime

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

  python systems-biology cobrapy escherichia-coli
  Python 12 5 3 0 Updated Jun 27, 2019

• cobrame

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

  python systems-biology computational-biology gene-expression metabolism cobra cobrapy
  Python 15 29 12 0 Updated Jan 11, 2019

• dynamicme

  Dynamic ME simulations (separate module)
  Python MIT 2 1 0 0 Updated Jan 10, 2019

• genbank_compare

  A repository for code that compares genbank files
  Jupyter Notebook 0 0 0 0 Updated Dec 17, 2018