Discover @rmcgibbo Open Source projects

Robert T. McGibbon (@rmcgibbo)

rmcgibbo

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Registered over 13 years ago
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Location 🇺🇸 United States
Country Total Rank 8,685
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slidedeck

Beautiful HTML5 slides in markdown. A easy-to-use fork of the google-io-2012 slide deck

npcuda-example

Example python (numpy) -- CUDA installable package with a C-extension library

jupyter-emacskeys

Emacs keybindings for Jupyter notebook

python-appveyor-conda-example

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

reftagger

Parse and tag unstructured academic citations.

pyhmc

Hamiltonain Monte Carlo in Python

logsumexp

Fast SSE logsumexp for python/numpy

figshare

Command line client for figshare

pyvdwsurface

Molecular (Van der Waals) surface.

sphinxcontrib-autodoc_doxygen

Sphinx / Doxygen bridge

covar

Compute shrinkage estimates of the covariance matrix

sphinxcontrib-lunrsearch

Instant search for Sphinx

mydra

openmm-webbuilder

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

async-priority-channel

mullermsm

Markov State Models on the Muller potential: a MSMBuilder Tutorial

r-rmcgibbo

resp2

RESP plugin for PSI4

openmm-cookbook

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

msmaccelerator2

Adaptive Sampling Markov State Model Driven Molecular Dynamics

Jarvis

execgraph

Parallel execution of shell commands with DAG dependencies

openmm-cmd

OpenMM Command Line Application

qchem-utils

Utilities for working with Q-Chem

information

Some information theory stuff -- transfer entropy, etc.

nixpkgs-hammering-action

projector

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

conda-hint

Hint generation for conda resolver.

history

An enhanced history(1) for bash

pypatchelf

Patchelf utility, packaged for python/pip

simtk.unit

ropen

hpcutils

Command line utilities for working remotely on HPC clusters.

msmbuilder3

Work on progress for next iteration of MSMBuilder

doccheck

Check that docstrings satisfy Numpy format

sudoku

Haskell Sudoku Solver

post-build-postgres

Nix post-build-hook to upload to postgresql

cache-dash-h

cache the help text for your dog-slow scripts

mutations

Notes (and code) on efficiently simulating mutants with MSMs

okbot

Respond to OkCupid messages with tweets.

fsync

Use your local GUI editor for remote development over SSH

opt-k

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

idle-trigger

Trigger a command when the CPUs are idle

circular_dichroism

prediction of cd spectra from structures

metric-learning

metric learning stuff

minimsmbuilder

hdf5pickle

Fast persistence of Python objects to HDF5 files

nixpkgs-hammering-action-example

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

GPURMSD

Yutong's GPU accelerated RMSD code

precedenceConstrainedKnapsack

Precedence constrained knapsack problem solver

cargo-remote

cargo subcommand to compile rust projects remotely

python-flake-utils

ipython_parallel_profiles

profiles for IPython.parallel

bibtex-resolver

holmes_rubin

Holmes-Rubin EM Estimator for Continuous-Time Markov processes

arduino

Personal arduino projects

tungsten

Parallel Markov State Model Acceleraed Molecular Dynamics

rmcgibbo-config

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

zmq-objc-framework

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

cctools-3.4.2-fork

Fork of cctools (workqueue) for MSMAccelerator

bagofwaves

rmcgibbo.org

professional website

wavekernel

oom-enospc-notify

Detect OOM and ENOSPC errors with BPF

kmeansrmsd

openmm-pulling

Pulling Simulation and Smoothing

openmm-builder

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

toy-systems

nebterpolator

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

openmm-debpackaging

adaptive-group-testing

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

neb

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

nix-unsafePlugins

This is unsafe. Don't use it.

gh-util

Github command line utilities

numpy-mypy