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ace

admission to candidacy exam

advanced-ml-project

autoencoding for fun and profit

automatic-state-decomposition

Automatic state decomposition Fortran90 code (outdated)

bar-for-bayes-factors

[incomplete, buggy] using BAR+MBAR for model comparsion

bqff

Bayesian quadrature and optimization with forcefields

cellfree-expression

Tools for cell-free expression of proteins

cgtools

Tools for developing coarse-graining schemes for Markov models

equilibrium-sampling-tinker

experiments and tinkering with equilibrium sampling methods

gp-accelerated-sampling

Using Gaussian Processes to accelerate sampling for forcefield parameterization

gpyopt

Gaussian Process Optimization using GPy

hugo-book

Hugo documentation theme as simple as plain book

izhikevich-model

Simulate a small network of simple, diverse spiking neurons and analyze results

mass-cytometry-vis

Visually query a mass cytometry dataset using a t-SNE map and Crossfilter

maxentile.github.io

mbar-variants

small experimental variations on MBAR

mbar_itic

Merging the MBAR and ITIC methodologies to optimize a TraPPE force switch model

mcmc-expectations

Tools for calculating expectations in a consistent way from MCMC samples

mcmc_zoo

exploring the zoo of MCMC algorithms

md-metric-learning

Benchmarking metric learning algorithms for constructing MSMs from molecular dynamics data

mdtraj

A modern, open library for the analysis of molecular dynamics trajectories

method-of-moments-tinker

implementing / tinkering with method of moments estimators for multi-view models

msm-learn

Learning how to learn Markov State Models of conformational dynamics

msm-pipeline

A pipeline for MSMs.

msm-theory-sandbox

A playground for examples and tools to explore the theory of MSMs and related models.

msmbuilder

Statistical models for biomolecular dynamics

msms

Markov state models

notebooks

Miscellaneous preliminary notebooks

onion

Find TIS layers from MSM in dynamical systems

onoma

generate silly names, then filter them using a markov model of word plausibility

openmmtools

Test systems for OpenMM