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@PNNL-Predictive-Phenomics PNNL Predictive Phenomics Initiative

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    35 repositories

    • DancePartner

      Public
      Mining multi-omics relationship networks from literature and databases
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Nov 11, 2025Nov 11, 2025

    • PIMLomics

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • crop

      Public
      Consistent Reproduction of Phenotype
      Python
      •
      MIT License
      •0•2•4•3•Updated Oct 24, 2025Oct 24, 2025

    • PTMPSI

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Oct 10, 2025Oct 10, 2025

    • ThermoOpt

      Public
      ThermoOpt: Thermodynamic optimization of metabolic models in dynamic environments through pathway confinement.
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Oct 8, 2025Oct 8, 2025

    • ProCaliper

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•7•3•1•Updated Sep 30, 2025Sep 30, 2025

    • ProteoMeter

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•3•2•0•Updated Aug 27, 2025Aug 27, 2025

    • Microbial-Isolate-LiP-Analysis

      Public
      Microbial Isolate Limited Proteolysis (LiP) Analysis Workflow
      proteomics-data-analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 28, 2025Jul 28, 2025

    • Viral-Experiment-LiP-Analysis

      Public
      Viral Experiment Limited Proteolysis (LiP) Analysis Workflow
      proteomics-data-analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jul 28, 2025Jul 28, 2025

    • .github

      Public
      0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • omicsTL

      Public
      Repo for the TIMED project code
      Python
      •
      Other
      •0•2•0•0•Updated Jul 14, 2025Jul 14, 2025

    • clean-contact

      Public
      Jupyter Notebook
      •
      Other
      •1•4•6•1•Updated Jun 2, 2025Jun 2, 2025

    • emll

      Public
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •4•4•17•5•Updated Apr 29, 2025Apr 29, 2025

    • biological_relationship_extraction

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Apr 17, 2025Apr 17, 2025

    • csc052-gem

      Public
      Shell
      •
      Apache License 2.0
      •0•2•3•3•Updated Mar 21, 2025Mar 21, 2025

    • csc009cyc

      Public
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

    • csc031cyc

      Public
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

    • csc040cyc

      Public
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

    • csc043cyc

      Public
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

    • csc052cyc

      Public
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Mar 21, 2025Mar 21, 2025

    • bspline_mutual_information

      Public
      Utility to bin continuous variables and estimate mutual information based on B-Spline binning.
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • carveme

      Public
      CarveMe: genome-scale metabolic model reconstruction
      Python
      •
      Other
      •58•0•3•1•Updated Nov 27, 2024Nov 27, 2024

    • concerto

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •2•3•13•3•Updated Oct 25, 2024Oct 25, 2024

    • csc009-gem

      Public
      HTML
      •0•1•4•3•Updated Oct 25, 2024Oct 25, 2024

    • csc031-gem

      Public
      Python
      •
      Apache License 2.0
      •0•1•3•3•Updated Oct 11, 2024Oct 11, 2024

    • eflux

      Public
      Jupyter Notebook
      •
      Other
      •1•2•8•1•Updated Oct 10, 2024Oct 10, 2024

    • csc040-gem

      Public
      Python
      •
      Apache License 2.0
      •0•0•1•2•Updated Sep 19, 2024Sep 19, 2024

    • csc043-gem

      Public
      Shell
      •
      Apache License 2.0
      •0•0•3•4•Updated Sep 19, 2024Sep 19, 2024

    • syn_bmca

      Public
      Code for implementing BMCA for Synechococcus elongatus
      Jupyter Notebook
      •
      Other
      •0•2•10•1•Updated Sep 19, 2024Sep 19, 2024

    • OptRollingup

      Public
      Exploring the differnt rolling up methods for protemics quantifications
      R
      •1•0•0•0•Updated Sep 17, 2024Sep 17, 2024