Repositories list

• celltraj

  Public
  Live-cell imaging cell-state trajectory embedding

  Python

  •

  MIT License

  •2•0•0•0•Updated Nov 2, 2024Nov 2, 2024

• 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 combinations.

  GNU General Public License v3.0

  •0•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•0•1•0•Updated Feb 17, 2024Feb 17, 2024

• BayesianBootstrap

  Public
  Python

  •2•4•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+ 1emcee

  Python

  •1•1•0•0•Updated May 6, 2023May 6, 2023

• pyGridSampler

  Public
  An adaptive grid-based sampling method using iterative batch sizes

  python3bayesiansampling+ 1mcmc

  Jupyter Notebook

  •

  MIT License

  •2•3•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 long-timescale kinetics by combining weighted ensemble simulation with Markov model “microstates” using non-Markovian theory, arXiv, (2020).

  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 Raman Subramanian, Rohith Palli, Maria Wu, and Daniel M. Zuckerman.

  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

• tablemc-proteins

  Public
  C++

  •0•0•0•0•Updated Feb 7, 2017Feb 7, 2017