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RudgeLab

We were a Synthetic Biology, Computational Biology and Complex Systems lab in the ICOS research group at Newcastle University run by Dr. Tim Rudge. The group has closed and these repos are no longer maintained, but are left here for reference.

Development of CellModeller continues in the CellModeller organization.

Development of Flapjack continues in the Flapjack organization.

Featured Software Tools

Genetic Design Automation: LOICA

Build Automation Control: PUDU

Data Management and Analysis: Flapjack

Bacterial Idividual Based Modelling: CellModeller

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  1. LOICA LOICA Public

    Logical Operators for Integrated Cell Algorithms

    Jupyter Notebook 8 4

  2. CellModeller CellModeller Public

    Forked from cellmodeller/CellModeller

    GPU-accelerated multicellular modelling framework

    Python 1 1

  3. Inverse_Characterization Inverse_Characterization Public

    Accurate Characterization of Dynamic Gene Expression and Growth Rate Profiles

    Jupyter Notebook

Repositories

Showing 10 of 35 repositories
  • .github Public

    Organization profile

    RudgeLab/.github's past year of commit activity
    0 MIT 0 0 0 Updated Sep 24, 2026
  • CellModeller Public Forked from cellmodeller/CellModeller

    GPU-accelerated multicellular modelling framework

    RudgeLab/CellModeller's past year of commit activity
    Python 1 56 0 1 Updated Aug 5, 2026
  • LOICA Public

    Logical Operators for Integrated Cell Algorithms

    RudgeLab/LOICA's past year of commit activity
    Jupyter Notebook 8 MIT 4 12 0 Updated Jul 31, 2026
  • PUDU Public

    Protocol Unified Design Unit

    RudgeLab/PUDU's past year of commit activity
    Python 6 MIT 1 19 (3 issues need help) 0 Updated Jul 14, 2026
  • popdyn Public

    Population dynamics

    RudgeLab/popdyn's past year of commit activity
    Jupyter Notebook 0 2 0 0 Updated May 26, 2026
  • brain Public

    Reservoir computing with coupled genetic oscillators

    RudgeLab/brain's past year of commit activity
    MATLAB 1 BSD-2-Clause 0 0 0 Updated Aug 2, 2024
  • napari-popdyn Public

    Napari plugin for quantitative population dynamics analysis

    RudgeLab/napari-popdyn's past year of commit activity
    Python 0 MIT 1 0 0 Updated Apr 4, 2024
  • GenePhLo Public

    Phase-based genetic logic circuit simulation

    RudgeLab/GenePhLo's past year of commit activity
    1 0 0 0 Updated Feb 15, 2024
  • FluoPi Public

    Code and teaching materials for UC/BackyardBrains raspberry pi "macro" scope.

    RudgeLab/FluoPi's past year of commit activity
    Jupyter Notebook 26 16 2 3 Updated Dec 30, 2023
  • CellModeller5 Public
    RudgeLab/CellModeller5's past year of commit activity
    C++ 0 MIT 0 0 0 Updated Aug 13, 2023

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