Skip to content

@JohnsonBiophysicsLab JohnsonBiophysicsLab

Change the repository type filter

All

    Repositories list

    12 repositories

    • ionerdss

      Public
      Python analysis and visualization tools for NERDSS
      simulationreaction-diffusionnerdss
      simulationreaction-diffusionnerdss
      Python
      •
      GNU General Public License v3.0
      •8•4•7•1•Updated Apr 9, 2026Apr 9, 2026

    • ionerdssPaperSI

      Public
      Simulation parameters and data used for generating figures in the paper.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • NERDSS

      Public
      NonEquilibrium Reaction-Diffusion Self-assembly Simulator
      simulationreaction-diffusionnon-equilibrium-dynamics
      simulationreaction-diffusionnon-equilibrium-dynamicsnerdss
      C++
      •
      GNU General Public License v3.0
      •11•3•2•0•Updated Feb 26, 2026Feb 26, 2026

    • munc13-cluster

      Public
      model of recruitment and clustering on the membrane. Python solves ODES, samples parameters to optimize loss function, agreement to experiment.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 4, 2026Jan 4, 2026

    • yeast_reassembly

      Public
      file storage for each yeast complex reassembly data and model
      0•0•0•0•Updated Dec 7, 2025Dec 7, 2025

    • membrane-selects-symmetric-growth-si

      Public
      This repository contains the supporting source code for graphing, analytical, and numerical calculations related to the continuum membrane model by Dr. Margaret…
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • DNA_protein_models

      Public
      Models to simulate protein binding to specific and nonspceific DNA, forming protein dimers and oligomers.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • OscillatorOptimization

      Public
      Julia package for optimizing oscillatory biological systems using Quality Diversity evolutionary algorithms
      Julia
      •
      MIT License
      •2•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • SLIMED

      Public
      Subdivision-limit membrane dynamics
      TeX
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • simulariumio

      Public
      Python package that converts simulation outputs to the format consumed by the Simularium viewer website
      Python
      •
      Apache License 2.0
      •7•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • FormatConvert

      Public
      Utility script for converting between file formats in NERDSS and ioNERDSS
      Python
      •
      MIT License
      •0•0•1•0•Updated Jun 17, 2025Jun 17, 2025

    • .github

      Public
      Contains documentations and README for the organization JohnsonBiophysicsLab
      0•0•0•0•Updated Jun 12, 2025Jun 12, 2025
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.