Skip to content

@JohnsonBiophysicsLab JohnsonBiophysicsLab

Change the repository type filter

All

    Repositories list

    11 repositories

    • 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

    • ionerdss

      Public
      Python analysis and visualization tools for NERDSS
      simulationreaction-diffusionnerdss
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •6•4•22•0•Updated Dec 18, 2025Dec 18, 2025

    • NERDSS

      Public
      NonEquilibrium Reaction-Diffusion Self-assembly Simulator
      simulationreaction-diffusionnon-equilibrium-dynamicsnerdss
      C++
      •
      GNU General Public License v3.0
      •10•3•2•0•Updated Dec 7, 2025Dec 7, 2025

    • 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 E Johnson lab, JHU.
      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
      •5•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