Pinned Repositories
Arduino-CmdMessenger
CmdMessenger Communication library for Arduino & .NET
biochem-jupyter-notebooks
interactive notebooks for teaching biochemistry concepts
client
Keybase Go Library, Client, Service, OS X, iOS, Android, Electron
md-analysis-tools
scripts for analyzing molecular dynamics trajectories using VMD
physical-biochemistry
course material for physical biochemistry class taught at the University of Oregon
PyCmdMessenger
Python interface for CmdMessenger arduino serial communication library
pyfx
Python library for adding visual effects to video streams
python-for-scientists
The easy way to set up Python for a scientist.
pythonic-science
Materials for Scientific Programming in Python Course at the UO
slidemachine
automatically generate reveal.js slides
harmsm's Repositories
harmsm/biochem-jupyter-notebooks
interactive notebooks for teaching biochemistry concepts
harmsm/physical-biochemistry
course material for physical biochemistry class taught at the University of Oregon
harmsm/align_fastq
Alignment or mapping of nucleotide sequencing reads
harmsm/asr-protocol
Protocol and scripts for doing ancestral sequence reconstruction
harmsm/bioconda-recipes
Conda recipes for the bioconda channel.
harmsm/BRENDApyrser
A Python parser for the BRENDA database
harmsm/ChiBio
ChiBio primary operating system.
harmsm/dms_tools2
software for the analysis and visualization of deep mutational scanning data
harmsm/eee
ensemble epistasis engine
harmsm/ElliptiC
analysis of rings for Pluth lab
harmsm/ElliptiCBn
tool for measuring ellipticity of cucurbituril macrocycles
harmsm/ete
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
harmsm/gpvolve
A Python API for computing evolutionary paths across genotype-phenotype maps and clustering of genotype-phenotype maps.
harmsm/kinetics_simulator
interactive notebooks for playing with simple Markov and Gillespie models for chemical reactions
harmsm/likelihood
Library for fitting models using a likelihood framework.
harmsm/lovoalign
harmsm/mdakit_sasa
Toolkit to calculate the surface accessible area of a molecular dynamic trajectory
harmsm/pastml
Ancestor character reconstruction and visualisation for rooted phylogenetic trees
harmsm/python-opentree
Python package for working with Open Tree of Life webservices and artifacts. Importable as opentree
harmsm/raxml-ng
RAxML Next Generation: faster, easier-to-use and more flexible
harmsm/scientific-posters
slides for workshop on making scientific posters
harmsm/scikit-bio
scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
harmsm/setup_md
Files and scripts used to set up MD simulations in the Harms Lab
harmsm/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
harmsm/topiary
Python framework for doing ancestral sequence reconstruction
harmsm/topiary-examples
Jupyter notebooks demonstrating the topiary ancestral sequence reconstruction package
harmsm/toyplot
Interactive plotting for Python.
harmsm/toyplot-feedstock
A conda-smithy repository for toyplot.
harmsm/toytree
A minimalist tree plotting library using toyplot graphs
harmsm/website
Website for the lab