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    36 repositories

    • WebCM

      Public
      WebCM is a web platform used to develop and run bacterial simulations
      pythonsimulationbiocomputing
      JavaScript
      •
      MIT License
      •1•0•1•0•Updated Jan 14, 2026Jan 14, 2026

    • popdyn

      Public
      Population dynamics
      Jupyter Notebook
      •1•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • LOICA

      Public
      Logical Operators for Integrated Cell Algorithms
      Jupyter Notebook
      •
      MIT License
      •2•6•12•0•Updated Jun 12, 2025Jun 12, 2025

    • PUDU

      Public
      Protocol Unified Design Unit
      Python
      •
      MIT License
      •1•5•19•0•Updated Oct 9, 2024Oct 9, 2024

    • brain

      Public
      Reservoir computing with coupled genetic oscillators
      MATLAB
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Aug 2, 2024Aug 2, 2024

    • napari-popdyn

      Public
      Napari plugin for quantitative population dynamics analysis
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 4, 2024Apr 4, 2024

    • CellModeller

      Public
      GPU-accelerated multicellular modelling framework
      Python
      •
      Other
      •51•1•0•1•Updated Feb 23, 2024Feb 23, 2024

    • GenePhLo

      Public
      Phase-based genetic logic circuit simulation
      0•1•0•0•Updated Feb 15, 2024Feb 15, 2024

    • FluoPi

      Public
      Code and teaching materials for UC/BackyardBrains raspberry pi "macro" scope.
      Jupyter Notebook
      •
      Other
      •16•26•2•3•Updated Dec 30, 2023Dec 30, 2023

    • CellModeller5

      Public
      C++
      •
      MIT License
      •0•0•0•0•Updated Aug 13, 2023Aug 13, 2023

    • InfoTracking

      Public
      Informt
      Jupyter Notebook
      •0•1•0•0•Updated Aug 8, 2023Aug 8, 2023

    • .github

      Public
      Organization profile
      MIT License
      •0•0•0•0•Updated Mar 9, 2023Mar 9, 2023

    • MiNuD

      Public
      Mitochondrial Nucleoids Distribution
      Python
      •
      MIT License
      •0•0•5•0•Updated Nov 28, 2022Nov 28, 2022

    • LOICA.jl

      Public
      LOICA but Julia
      Julia
      •
      MIT License
      •1•1•0•0•Updated Aug 9, 2022Aug 9, 2022

    • Inverse_Characterization

      Public
      Accurate Characterization of Dynamic Gene Expression and Growth Rate Profiles
      Jupyter Notebook
      •
      MIT License
      •0•0•4•0•Updated Jul 25, 2022Jul 25, 2022

    • killifish

      Public
      CellModeller model files, analysis notebooks, and scripts for modeling annual killifish.
      Jupyter Notebook
      •0•2•0•0•Updated Jun 6, 2022Jun 6, 2022

    • SpatialOscillator

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 12, 2021Feb 12, 2021

    • Corchea-1

      Public
      Paper-fluidic open science hardware for research, teaching and more
      Jupyter Notebook
      •1•0•0•0•Updated Jan 6, 2021Jan 6, 2021

    • pyrite

      Public
      Analysis code for studying bacterial colony formation on pyrite
      0•0•0•0•Updated Aug 18, 2020Aug 18, 2020

    • corcheaweb

      Public
      Landing page for Corchea's project
      HTML
      •0•0•0•0•Updated May 21, 2020May 21, 2020

    • Corchea

      Public
      Hardware control and analysis for Corchea paper flow device
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 4, 2020Jan 4, 2020

    • CMStatPhys

      Public
      Statistical physics analysis of CellModeller simulations
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 25, 2019Aug 25, 2019

    • MorphoOrganismos

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Nov 5, 2018Nov 5, 2018

    • final-project-ptbravo

      Public
      final-project-ptbravo created by GitHub Classroom
      Python
      •1•0•0•0•Updated Jun 30, 2018Jun 30, 2018

    • final-project-ajananias

      Public
      final-project-ajananias created by GitHub Classroom
      0•0•0•0•Updated Jun 27, 2018Jun 27, 2018

    • final-project-Prosimio

      Public
      final-project-Prosimio created by GitHub Classroom
      0•0•0•0•Updated Jun 4, 2018Jun 4, 2018

    • final-project-cghernandez

      Public
      final-project-cghernandez created by GitHub Classroom
      0•0•0•0•Updated Jun 4, 2018Jun 4, 2018

    • piv

      Public
      Particle image velocimetry for tracking movement and growth of cells.
      Jupyter Notebook
      •1•1•0•0•Updated Apr 6, 2018Apr 6, 2018

    • Inverters

      Public
      Code and notebooks to analyze data from plate reader assays which involves proteic and CRISPRi inverters
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Nov 8, 2017Nov 8, 2017

    • Tutorials

      Public
      Programming, image processing, data analysis, and other tutorials for the lab
      Jupyter Notebook
      •0•0•0•0•Updated Aug 28, 2017Aug 28, 2017