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    26 repositories

    • SMLT_sequencing

      Public
      Processing the sequencing data from the Smlt1473 project
      Shell
      •1•0•0•0•Updated Feb 16, 2026Feb 16, 2026

    • Persister_project

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • reconstructor

      Public
      Reconstructor: a COBRApy-compatible python tool for the automated reconstruction of genome-scale metabolic models
      software
      software
      Python
      •
      MIT License
      •1•2•3•0•Updated Dec 5, 2025Dec 5, 2025

    • Ileum1-and-RIA

      Public
      Code and data required to reproduce analysis from "Metabolic network analysis of Crohn’s disease reveals sex- and age-specific cellular phenotypes"
      HTML
      •1•1•0•0•Updated Sep 18, 2025Sep 18, 2025

    • Jenior_FMT_2022

      Public
      0•0•0•0•Updated Jun 5, 2022Jun 5, 2022

    • Jenior_FMTconsortia

      Public
      Updated
      R
      •
      MIT License
      •1•0•0•0•Updated Jun 5, 2022Jun 5, 2022

    • Jenior_FMTconsortia_2022

      Public
      R
      •
      MIT License
      •1•2•0•0•Updated Jun 5, 2022Jun 5, 2022

    • Jenior_CdifficileGENRE_2021

      Public
      Repository associated with C. difficile GENRE publication
      HTML
      •
      MIT License
      •0•1•0•0•Updated Oct 19, 2021Oct 19, 2021

    • iCardio

      Public
      Code associated with the iCardio publication
      MATLAB
      •4•4•1•0•Updated Feb 15, 2021Feb 15, 2021

    • Cardiotoxicity

      Public
      empty
      empty
      0•0•0•0•Updated Oct 6, 2020Oct 6, 2020

    • Jenior_RIPTiDe_2020

      Public
      Repository associated with RIPTiDe publication
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Sep 2, 2020Sep 2, 2020

    • platereader

      Public
      Designs for a miniaturized plate reader for high-throughput phenotypic screening.
      SMT
      •0•8•0•0•Updated Feb 7, 2020Feb 7, 2020

    • hepatocyte_omicsdata

      Public
      Code to analyze transcriptomics, metabolomics, and TIMBR data
      R
      •0•2•0•0•Updated May 3, 2019May 3, 2019

    • iSIM

      Public
      Python, R, and Matlab code relating to the iSIM manuscript
      Python
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Jan 9, 2019Jan 9, 2019

    • P_aeruginosa_recon

      Public
      Shell
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Dec 18, 2018Dec 18, 2018

    • P_syringae_recon

      Public
      Project is in separate private repository
      HTML
      •0•0•0•0•Updated Nov 8, 2018Nov 8, 2018

    • CSBL_code_repository

      Public
      Repository for shared programmatic code from the Papin lab at UVA
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 30, 2018Aug 30, 2018

    • Chloroquine-Project

      Public
      R
      •0•0•0•0•Updated Aug 22, 2018Aug 22, 2018

    • ABResistancePA01Py

      Public
      Python scripts for gene essentiality analysis.
      Python
      •0•0•0•0•Updated Oct 10, 2017Oct 10, 2017

    • ABResistancePA01MAT

      Public
      Software for research into the metabolic network and gene essentiality changes during antibiotic resistence formation in the pathogen Psuedomonas Aeruginosa.
      MATLAB
      •0•0•0•0•Updated Aug 1, 2017Aug 1, 2017

    • ToyConMAT

      Public
      MATLAB implementation of the toycon1 metabolic model.
      M
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jul 31, 2017Jul 31, 2017

    • ToyConPy

      Public
      Python
      •0•0•0•0•Updated Jul 31, 2017Jul 31, 2017

    • SteadyComPy

      Public
      A cobrapy-based implementation of SteadyCom
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 27, 2017Jul 27, 2017

    • CoculturePlate

      Public
      All files for the vertical membrane co-culture plate project
      MATLAB
      •0•0•0•0•Updated May 22, 2017May 22, 2017

    • ratcon1

      Public
      Reconciled rat and human metabolic networks for comparative toxicogenomics analyses and biomarker predictions
      R
      •3•7•0•0•Updated Feb 8, 2017Feb 8, 2017

    • PlateReaderCode

      Public
      C++
      •2•0•0•0•Updated Jun 23, 2014Jun 23, 2014
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