ryancoleman

2D-protein-shape-matching

find 2d views of proteins that look like your favorite shape

algorithms

module of algorithms for Python

analysis-scripts

Some simple scripts for analyzing lists of data, both paired & unpaired.

auto-dud-e

Auto-DUD-E is a website for a test set of ligands & decoys for molecular docking.

autodock-vina

fork of autodock vina, from http://vina.scripps.edu/

FindingKnottedAndLinkedVorticityLinesIn3DVectorFields

code from my master's thesis work. has sat in a backup folder for a decade. might be useful? java viewer seems nonfunctional as Java3D seems dead.

lotsofcoresbook1code

Code repo for lotsofcores.com book 1, here since dropbox doesn't work for everyone

lotsofcoresbook2code

mirror from http://lotsofcores.com book 2, since dropbox isn't good for everyone

mol2db2

mol2db2 is a python program that takes various ligand files and turns them into a .db2 database for docking with DOCK.

traveldistance

Github version of Travel Distance code by me (Ryan Coleman) and my advisor (Kim Sharp). See http://crystal.med.upenn.edu/travel_distance.html for official download, academic paper references, license, etc.

ryancoleman/lotsofcoresbook2code

mirror from http://lotsofcores.com book 2, since dropbox isn't good for everyone

ryancoleman/lotsofcoresbook1code

Code repo for lotsofcores.com book 1, here since dropbox doesn't work for everyone

ryancoleman/2D-protein-shape-matching

find 2d views of proteins that look like your favorite shape

ryancoleman/traveldistance

Github version of Travel Distance code by me (Ryan Coleman) and my advisor (Kim Sharp). See http://crystal.med.upenn.edu/travel_distance.html for official download, academic paper references, license, etc.

ryancoleman/Apollo-11

Original Apollo 11 guidance computer (AGC) source code digitized by folks at Virtual AGC (http://www.ibiblio.org/apollo/) and MIT Museum.

ryancoleman/Byfl

Program analysis tool based on software performance counters

ryancoleman/card_codex

Magic: the Gathering card similarity search

ryancoleman/conceptnet5

Code for building ConceptNet from raw data.

ryancoleman/daal

ryancoleman/DeepMind-Atari-Deep-Q-Learner

The original code from the DeepMind article + my tweaks

ryancoleman/ea-thesaurus

The Edinburgh Associative Thesaurus (EAT) is a set of word association norms showing the counts of word association as collected from subjects.

ryancoleman/gemrb

Engine Made with preRendered Background

ryancoleman/git-lfs

Git extension for versioning large files

ryancoleman/GitTorrent

A decentralization of GitHub using BitTorrent and Bitcoin

ryancoleman/linux

run Linux on Yosemite easily from the CLI

ryancoleman/merge_watermark_pdf

using pypdf2 to merge and watermark some pdfs

ryancoleman/NASTRAN

NASTRAN is the NASA Structural Analysis System, a finite element analysis program (FEA)

ryancoleman/NASTRAN-95

ryancoleman/openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

ryancoleman/paper-now

Create, edit and display a journal article, entirely in GitHub

ryancoleman/process_magazine_index_to_html

a very custom bunch of python code to process a very specific excel files into some HTML webpages.

ryancoleman/PubMed

PubMed analysis: code and data

ryancoleman/PyPDF2

A utility to read and write PDFs with Python

ryancoleman/rbspy

Sampling profiler for Ruby

ryancoleman/SF5eSRD

A little private project where I replace all the fantasy stuff in the Dungeons & Dragons 5th edition SRD with sci-fi stuff. Based on https://5thsrd.org/ Website for this repository can be found here:

ryancoleman/simplequiz

Very old code for someone else to borrow

ryancoleman/spack

A flexible package manager designed to support multiple versions, configurations, platforms, and compilers.

ryancoleman/StickerConstructorSpec

The Sticker Constructor Specification

ryancoleman/ub-canaries

collection of C/C++ programs that try to get compilers to exploit undefined behavior

ryancoleman/unix-history-repo