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blogscripts

Repository for code used in my blog posts

cythongsl

Cython interface for the GNU Scientific Library (GSL).

datreant.core

persistent, pythonic trees for heterogeneous data

datreant.data

Convenient data storage and retrieval for Treants

depimaging

For (post-)processing of microscopy/imaging data from DEP experiments.

examples

Code examples from the book.

fireworks

The Fireworks Workflow Management Repo.

github-for-developers-7

gromacswrapper

GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into python scripts. This is generally superior to shell scripts because of python’s better error handling and superior data structures. It also allows for modularization and code re-use. In addition, commands, warnings and errors are logged to a file so that there exists a complete history of what has been done.

hermeshd

HERMESHD is a discontinuous Galerkin 3D fluctuating hydrodynamics code for nanoscale fluid simulation

lammps

Public development project of the LAMMPS MD software package

mastering-pycharm-course

Course demos and handouts for Talk Python's Effective PyCharm course

mdanalysis

MDAnalysis is a Python toolkit to analyze molecular dynamics trajectories.

mdanalysis.github.io

MDAnalysis home page mdanalysis.org as GitHub pages.

mdsynthesis

a logistics and persistence engine for the analysis of molecular dynamics trajectories

mdworks

molecular dynamics, with Fireworks!

molecalc

MoleCalc is a web interface that allows anyone to build molecules and calculate molecular properties online

molecalc-2.0

mongodb-quickstart-course

Course demos and handout material for Talk Python's MongoDB Quickstart course

numba_tutorial_scipy2016

Numba tutorial materials for Scipy 2016

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

ppqm

Enable cheminformatics and quantum chemistry

psanalysis

Quantify the geometric and atomistic similarity of conformational transition pathways

psanalysistutorial

Examples and data for performing path similarity analysis (PSA).

scipy-2015-cython-tutorial

Content for the SciPy 2015 Cython tutorial: http://www.scipy2015.scipy.org/ehome/115969/289057/?&

scipy-2016

abstract submission and presentation materials for SciPy 2016

scipy-2017-cython-tutorial

Material for the SciPy 2017 Cython tutorial

scipy2013-cython-tutorial

scipy_proceedings

SciPy conference proceedings: MDAnalysis paper

seaborn

Statistical data visualization using matplotlib