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@ModelEngineering Model Engineering

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    26 repositories

    • linearity_analysis

      Public
      Address how linear is BioModels.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 26, 2026Aug 26, 2026

    • deprecated_model_linearity_analysis

      Public
      Analyzes the accuracy of a linear approximation for model kinetics
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 7, 2026Jun 7, 2026

    • SBMLModel

      Public
      Infrastructure for doing analysis using the python package Tellurium for simulations in Systems Biology
      Python
      •
      MIT License
      •0•0•0•0•Updated May 13, 2026May 13, 2026

    • autoencodersb

      Public
      Creation and analysis of Information Planes for Deep Neural Networks
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

    • pystablesb

      Public
      Package that adds reactions to a network to either stabilize or destablize the network.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 4, 2026Mar 4, 2026

    • crn_subsystems

      Public
      Analysis of subsystems of chemical reaction networks
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 21, 2025Dec 21, 2025

    • controlSBML

      Public
      Analyze and design feedback control for SBML models
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Dec 6, 2025Dec 6, 2025

    • BIOEN-437

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 17, 2025Nov 17, 2025

    • pySubnetSB

      Public
      Structurally identical reaction networks
      Jupyter Notebook
      •
      MIT License
      •0•1•1•0•Updated Aug 2, 2025Aug 2, 2025

    • iBuilderSB

      Public
      Intelligent construction of models for system biology
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

    • ExplorerSB

      Public
      Explore models in systems biology
      Component Pascal
      •
      MIT License
      •0•2•0•0•Updated Oct 28, 2024Oct 28, 2024

    • SBMLKinetics

      Public
      Repository of tests to validate kinetics expressions in SBML models.
      Python
      •
      MIT License
      •2•1•0•0•Updated Apr 23, 2024Apr 23, 2024

    • dash

      Public
      Exploring the use of dash as a front end for Biosimulations
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 2, 2023Dec 2, 2023

    • Oscillators

      Public
      Investigation of oscillations in reaction networks
      Jupyter Notebook
      •0•0•0•0•Updated Nov 23, 2023Nov 23, 2023

    • fitterpp

      Public
      Extended fitter for fitting parameters.
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2022Dec 18, 2022

    • smarte

      Public
      Smart Parameter Estimation in Reaction Networks
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 13, 2022Dec 13, 2022

    • SBMLLint

      Public
      Model checker for SBML compliant models.
      Python
      •
      MIT License
      •3•2•4•1•Updated Nov 22, 2022Nov 22, 2022

    • advancing-biomedical-models

      Public
      Topics course on tools for kinetics modeling
      Jupyter Notebook
      •
      MIT License
      •6•3•0•0•Updated Oct 19, 2022Oct 19, 2022

    • SBdoe

      Public
      Tool for designing and running computational experiments in systems biology.
      MIT License
      •0•0•0•0•Updated Aug 27, 2022Aug 27, 2022

    • smart-antimony-vscode

      Public
      A smart editor and recommender interface for VScode
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Oct 20, 2021Oct 20, 2021

    • km_unit

      Public
      Unit testing for kinetics models
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Aug 4, 2020Aug 4, 2020

    • Model-Testing

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 24, 2020Jul 24, 2020

    • memote

      Public
      memote – the genome-scale metabolic model test suite
      HTML
      •
      Apache License 2.0
      •32•0•0•0•Updated Apr 22, 2020Apr 22, 2020

    • SBMLLintSave

      Public
      Saved folders from SBMLLint
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 1, 2020Apr 1, 2020

    • TemplateSB

      Public
      Template preprocessor for kinetics models.
      Python
      •
      MIT License
      •0•1•4•0•Updated Nov 16, 2018Nov 16, 2018

    • ModelAnalysis

      Public
      Analysis of kinetics models
      Python
      •
      MIT License
      •0•0•3•0•Updated Sep 12, 2017Sep 12, 2017
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