Discover rmcgibbo/okbot 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

async-priority-channel

Markov State Models on the Muller potential: a MSMBuilder Tutorial

mullermsm

r-rmcgibbo

resp2

openmm-cookbook

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

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.

Work on progress for next iteration of MSMBuilder

msmbuilder3

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

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