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    31 repositories

    • rite_weight

      Public
      A lightweight Python package for computing steady-state weights from short trajectory segments.
      Python
      •
      MIT License
      •1•5•0•0•Updated Aug 31, 2026Aug 31, 2026

    • CodingClass2026

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 28, 2026Jul 28, 2026

    • WE_variance_minimization

      Public
      Python
      •1•2•0•0•Updated Mar 4, 2026Mar 4, 2026

    • CodingClass2025

      Public
      Materials for summer 2025 class for high-school students
      Jupyter Notebook
      •0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

    • Bayesian_hierarchical_ITC

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • CellTrajAnl

      Public
      Analysis of cell state transition dynamics from the brightfield microscopy images of MCF10A cells treated with ligands EGF, OSM, TGF-beta, and their combination…
      GNU General Public License v3.0
      •0•1•0•0•Updated Jan 19, 2025Jan 19, 2025

    • msm_we

      Public
      This is a package for doing history-augmented MSM (haMSM) analysis on weighted ensemble trajectories.
      Python
      •
      MIT License
      •1•2•1•0•Updated Nov 19, 2024Nov 19, 2024

    • celltraj

      Public
      Live-cell imaging cell-state trajectory embedding
      Python
      •
      MIT License
      •2•0•0•0•Updated Nov 2, 2024Nov 2, 2024

    • coding2024

      Public
      Materials for introductory coding class - Summer 2024
      Jupyter Notebook
      •3•0•0•0•Updated Jul 26, 2024Jul 26, 2024

    • ModelExplorer

      Public
      Perl
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 17, 2024Feb 17, 2024

    • Bayesian_Transporter

      Public
      Transporter mechanism identification using Bayesian inference
      Jupyter Notebook
      •1•1•1•0•Updated Feb 17, 2024Feb 17, 2024

    • BayesianBootstrap

      Public
      Python
      •2•5•0•1•Updated Jan 29, 2024Jan 29, 2024

    • Bayesian_Transporter_Paper

      Public archive
      Transporter mechanism identification using Bayesian inference
      Jupyter Notebook
      •1•0•0•0•Updated Sep 22, 2023Sep 22, 2023

    • pyPAM

      Public
      A parallel extension of the affine invariant ensemble sampler w/ optional ensemble mixing
      pythonbayesianmcmc
      pythonbayesianmcmcemcee
      Python
      •1•1•0•0•Updated May 6, 2023May 6, 2023

    • pyGridSampler

      Public
      An adaptive grid-based sampling method using iterative batch sizes
      python3bayesiansampling
      python3bayesiansamplingmcmc
      Jupyter Notebook
      •
      MIT License
      •3•5•2•0•Updated Apr 8, 2023Apr 8, 2023

    • Bayesian_ITC

      Public
      Notebook for Bayesian analysis of isothermal titration calorimetry using a two-step binding model
      Jupyter Notebook
      •0•1•0•0•Updated Mar 9, 2023Mar 9, 2023

    • sampler_survey

      Public
      Jupyter Notebook
      •
      ISC License
      •0•0•0•0•Updated Oct 18, 2022Oct 18, 2022

    • codeclass

      Public
      Lessons for code class
      Jupyter Notebook
      •1•0•0•0•Updated Jul 29, 2022Jul 29, 2022

    • NMpathAnalysis

      Public
      Jupyter Notebook
      •
      MIT License
      •4•3•1•1•Updated Mar 2, 2022Mar 2, 2022

    • EM_OligomerAnalysis

      Public
      Python
      •0•0•0•0•Updated Jan 20, 2022Jan 20, 2022

    • T32_Nanocourse

      Public
      Code and supporting sample data for the T32 Quantitative Biology of Cancer nanocourse
      Jupyter Notebook
      •1•0•0•0•Updated Oct 19, 2021Oct 19, 2021

    • phat

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 8, 2021Oct 8, 2021

    • Bayesian_Analysis

      Public
      Workbook for Bayesian analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•4•0•Updated May 17, 2021May 17, 2021

    • msmWE

      Public
      Implementation of history-augmented Markov State Model building from Weighted Ensemble simulation data, see Copperman and Zuckerman, Accelerated estimation of l…
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 30, 2020Nov 30, 2020

    • best-practices

      Public
      Best practices and lessons learned in the Zuckerman group
      1•0•0•0•Updated Dec 20, 2019Dec 20, 2019

    • Random-Walk-MSD

      Public
      0•0•0•0•Updated Sep 7, 2019Sep 7, 2019

    • mrmc-paper-data

      Public
      Minimal data set for paper "Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α” by Justin Spiriti, Sundar Ra…
      Python
      •0•0•0•0•Updated Jan 30, 2019Jan 30, 2019

    • WESTPA_Scripts

      Public
      0•0•0•0•Updated Sep 17, 2018Sep 17, 2018

    • tablemc-virus

      Public
      C++
      •0•0•0•0•Updated Apr 30, 2018Apr 30, 2018

    • mrmc

      Public
      Mixed Resolution Monte Carlo simulation
      C++
      •2•1•0•0•Updated Mar 7, 2018Mar 7, 2018
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