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notebooks Public
Miscellaneous preliminary notebooks
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mbar-variants Public
small experimental variations on MBAR
Python Apache License 2.0 UpdatedJul 28, 2023 -
izhikevich-model Public
Simulate a small network of simple, diverse spiking neurons and analyze results
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timemachine Public
Forked from proteneer/timemachineDifferentiate all the things!
Python Other UpdatedSep 18, 2020 -
hugo-book Public
Forked from alex-shpak/hugo-bookHugo documentation theme as simple as plain book
HTML MIT License UpdatedApr 19, 2020 -
msm-learn Public
Learning how to learn Markov State Models of conformational dynamics
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MBAR_ITIC Public
Forked from ramess101/MBAR_ITICMerging the MBAR and ITIC methodologies to optimize a TraPPE force switch model
Python UpdatedAug 17, 2017 -
openmmtools Public
Forked from choderalab/openmmtoolsTest systems for OpenMM
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wivaprec Public
[work-in-progress] Find a change-of-variables that makes your MCMC problem easier
Python MIT License UpdatedApr 27, 2017 -
mdtraj Public
Forked from mdtraj/mdtrajA modern, open library for the analysis of molecular dynamics trajectories
C GNU Lesser General Public License v2.1 UpdatedFeb 9, 2017 -
radical.ensemblemd Public
Forked from radical-cybertools/radical.entkThe Radical Ensemble Molecular Dynamics (MD) Toolkit
Python MIT License UpdatedOct 21, 2016 -
msmbuilder Public
Forked from msmbuilder/msmbuilderStatistical models for biomolecular dynamics
Python GNU Lesser General Public License v2.1 UpdatedOct 20, 2016 -
msm-theory-sandbox Public
Forked from markovmodel/msm-theory-sandboxA playground for examples and tools to explore the theory of MSMs and related models.
MIT License UpdatedOct 18, 2016 -
PyEMMA Public
Forked from markovmodel/PyEMMAPython API for Emma's Markov Model Algorithms
Python GNU Lesser General Public License v3.0 UpdatedOct 17, 2016 -
cgtools Public
Tools for developing coarse-graining schemes for Markov models
Python MIT License UpdatedOct 3, 2016 -
onion Public
Forked from choderalab/onionFind TIS layers from MSM in dynamical systems
Jupyter Notebook UpdatedAug 2, 2016 -
automatic-state-decomposition Public
Forked from choderalab/automatic-state-decompositionAutomatic state decomposition Fortran90 code (outdated)
Fortran UpdatedMay 15, 2016 -
msm-pipeline Public
Forked from choderalab/msm-pipelineA pipeline for MSMs.
Python UpdatedMay 12, 2016 -
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MSMs Public
Forked from choderalab/MSMsMarkov state models
Jupyter Notebook GNU General Public License v2.0 UpdatedMar 9, 2016 -
openpathsampling Public
Forked from openpathsampling/openpathsamplingAn open source Python framework for transition interface and path sampling calculations.
Python GNU Lesser General Public License v2.1 UpdatedMar 3, 2016 -
mcmc-expectations Public
Tools for calculating expectations in a consistent way from MCMC samples
Jupyter Notebook UpdatedFeb 18, 2016 -
bar-for-bayes-factors Public
[incomplete, buggy] using BAR+MBAR for model comparsion
Jupyter Notebook UpdatedFeb 16, 2016 -
method-of-moments-tinker Public
implementing / tinkering with method of moments estimators for multi-view models
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yank Public
Forked from choderalab/yankGPU-accelerated calculation of ligand binding affinities in implicit and explicit solvent using alchemical free energy methodologies
Python GNU Lesser General Public License v3.0 UpdatedJan 26, 2016 -
cellfree-expression Public
Forked from choderalab/cellfree-expressionTools for cell-free expression of proteins
Python UpdatedDec 9, 2015 -
equilibrium-sampling-tinker Public
experiments and tinkering with equilibrium sampling methods
Python MIT License UpdatedNov 16, 2015 -
onoma Public
generate silly names, then filter them using a markov model of word plausibility
Python MIT License UpdatedSep 26, 2015
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