Discover rmcgibbo/msmbuilder3 Open Source project

Demo project for building and shipping Python conda packages with Appveyor CI and Travis CI

python-appveyor-conda-example

PowerShell

reftagger

Parse and tag unstructured academic citations.

Hamiltonain Monte Carlo in Python

pyhmc

Fast SSE logsumexp for python/numpy

logsumexp

figshare

Command line client for figshare

Molecular (Van der Waals) surface.

pyvdwsurface

sphinxcontrib-autodoc_doxygen

Sphinx / Doxygen bridge

Compute shrinkage estimates of the covariance matrix

covar

Instant search for Sphinx

sphinxcontrib-lunrsearch

mydra

JS/HTML5 webapp for setting up custom GPU-accelerated OpenMM molecular dynamics simulations.

openmm-webbuilder

JavaScript

mullermsm

Markov State Models on the Muller potential: a MSMBuilder Tutorial

A collection of code snippets for doing molecular simulations with OpenMM.

async-priority-channel

r-rmcgibbo

resp2

openmm-cookbook

msmaccelerator2

Adaptive Sampling Markov State Model Driven Molecular Dynamics

Jarvis

Parallel execution of shell commands with DAG dependencies

execgraph

OpenMM Command Line Application

openmm-cmd

Utilities for working with Q-Chem

qchem-utils

Some information theory stuff -- transfer entropy, etc.

information

nixpkgs-hammering-action

Interactive plotting of MD projections + molecular viewer with HTML5 and WebGL

projector

JavaScript

conda-hint

Hint generation for conda resolver.

An enhanced history(1) for bash

history

Patchelf utility, packaged for python/pip

pypatchelf

simtk.unit

ropen

hpcutils

Command line utilities for working remotely on HPC clusters.

Check that docstrings satisfy Numpy format

doccheck

Nix post-build-hook to upload to postgresql

sudoku

Haskell Sudoku Solver

Haskell

post-build-postgres

cache the help text for your dog-slow scripts

cache-dash-h

Notes (and code) on efficiently simulating mutants with MSMs

mutations

Respond to OkCupid messages with tweets.

okbot

Use your local GUI editor for remote development over SSH

fsync

Shell

opt-k

Likelihood framework for choosing the optimal number of states in a Markov State Model

TeX

idle-trigger

Trigger a command when the CPUs are idle

prediction of cd spectra from structures

circular_dichroism

metric-learning

metric learning stuff

minimsmbuilder

Fast persistence of Python objects to HDF5 files

hdf5pickle

See https://github.com/rmcgibbo/nixpkgs-hammering-action

nixpkgs-hammering-action-example

Nix

GPURMSD

Yutong's GPU accelerated RMSD code

Precedence constrained knapsack problem solver

precedenceConstrainedKnapsack

cargo subcommand to compile rust projects remotely

cargo-remote

profiles for IPython.parallel

python-flake-utils

Nix

ipython_parallel_profiles

bibtex-resolver

Holmes-Rubin EM Estimator for Continuous-Time Markov processes

holmes_rubin

Personal arduino projects

arduino

Processing

tungsten

Parallel Markov State Model Acceleraed Molecular Dynamics

My config files (bashrcs, etc) to be synced across machines

rmcgibbo-config

Emacs Lisp

zmq-objc-framework

Objective-C binding for ZeroMQ. Fork of https://github.com/jeremy-w/objc-zmq

Shell

cctools-3.4.2-fork

Fork of cctools (workqueue) for MSMAccelerator

bagofwaves

rmcgibbo.org

wavekernel

oom-enospc-notify

Detect OOM and ENOSPC errors with BPF

Pulling Simulation and Smoothing

kmeansrmsd

openmm-pulling

A graphical interface for building (and now running!) OpenMM scripts

openmm-builder

toy-systems

Interpolator for generating smooth paths from an ab-intio MD trajectory for NEB calculations.

nebterpolator

https://en.wikipedia.org/wiki/Group_testing#Generalised_binary-splitting_algorithm

openmm-debpackaging

Shell

adaptive-group-testing

OpenMM Nudged Elastic Band (NEB) Plugin. Currently only supports steepest descent optimization -- needs a little to switch to a quasti-newton optimizer.

neb

This is unsafe. Don't use it.

nix-unsafePlugins

Github command line utilities

gh-util

numpy-mypy