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@caseywdunn
caseywdunn / docker.md
Last active Jul 8, 2019
Docker cheat sheet
View docker.md

Docker cheat sheet

Introduction

Docker is a tool for bundling together applications and their dependencies into images that can than be run as containers on many different types of computers. This is useful to scientists because:

  • It greatly simplifies distribution and installation of complex work flows that have many interacting components.
@peci1
peci1 / Abbreviate Journal Names in Bibtex Database.py
Last active Sep 25, 2017 — forked from FilipDominec/Abbreviate Journal Names in Bibtex Database.py
Using the translation table from the Jabref program, finds and replaces all scientific journal names to their standardized abbreviated form. First argument is the file to be processed; outputs safely to 'abbreviated.bib'
View Abbreviate Journal Names in Bibtex Database.py
#!/usr/bin/env python
#-*- coding: utf-8 -*-
import sys, os
import re
try: bibtexdb = open(sys.argv[1]).read()
except: print "Error: specify the file to be processed!"
if not os.path.isfile('journalList.txt'):
@hrldcpr
hrldcpr / tree.md
Last active Jul 26, 2019
one-line tree in python
View tree.md

One-line Tree in Python

Using Python's built-in defaultdict we can easily define a tree data structure:

def tree(): return defaultdict(tree)

That's it!

@brantfaircloth
brantfaircloth / gist:895282
Created Mar 30, 2011
Substitution models in mrbayes
View gist:895282

##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma

##SYM

lset applyto=() nst=6                           # SYM
prset applyto=() statefreqpr=fixed(equal)
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