ehazlett

#!/usr/bin/env python
# numpy and biopython are required -- pip install numpy biopython

from Bio import Entrez
from Bio import Medline

MAX_COUNT = 10
TERM = 'Tuberculosis'

print('Getting {0} publications containing {1}...'.format(MAX_COUNT, TERM))

smukkejohan

# Python port of Paul Bourke's http://local.wasp.uwa.edu.au/~pbourke/fractals/lyapunov/gen.c
# By Johan Bichel Lindegaard - http://johan.cc

import math
import random
from PIL import Image, ImageDraw
import argparse
import os

parser = argparse.ArgumentParser(description='Search for chaos.')

iamatypeofwalrus

What

Roll your own iPython Notebook server with Amazon Web Services (EC2) using their Free Tier.

What are we using? What do you need?

• An active AWS account. First time sign-ups are eligible for the free tier for a year
• One Micro Tier EC2 Instance
• With AWS we will use the stock Ubuntu Server AMI and customize it.
• Anaconda for Python.
• Coffee/Beer/Time

fomightez

# code by Steven H. D. Haddock and Casey W. Dunn as described in:
# Practical Computing for Biologists
# Steven H. D. Haddock and Casey W. Dunn
# Published in 2011 by Sinauer Associates.
# ISBN 978-0-87893-391-4
# http://www.sinauer.com/practical-computing-for-biologists.html
# see practicalcomputing.org
#
#scripts freely available by the original authors at practicalcomputing.org
#DIRECT LINK: http://practicalcomputing.org/files/pcfb_examples.zip

fomightez

fomightez

# code by Steven H. D. Haddock and Casey W. Dunn as described in:
# Practical Computing for Biologists
# Steven H. D. Haddock and Casey W. Dunn
# Published in 2011 by Sinauer Associates.
# ISBN 978-0-87893-391-4
# http://www.sinauer.com/practical-computing-for-biologists.html
# see practicalcomputing.org
#
#scripts freely available by the original authors at practicalcomputing.org
#DIRECT LINK: http://practicalcomputing.org/files/pcfb_examples.zip

fomightez

minrk

#!/usr/bin/env python
"""strip outputs from an IPython Notebook

Opens a notebook, strips its output, and writes the outputless version to the original file.

Useful mainly as a git filter or pre-commit hook for users who don't want to track output in VCS.

This does mostly the same thing as the `Clear All Output` command in the notebook UI.

LICENSE: Public Domain

sloria

The Best of the Best Practices (BOBP) Guide for Python

A "Best of the Best Practices" (BOBP) guide to developing in Python.

In General

Values

• "Build tools for others that you want to be built for you." - Kenneth Reitz
• "Simplicity is alway better than functionality." - Pieter Hintjens

langner

"""Tools for searching Pubmed for a list of PMIDs.

The goal here is to search for many PMIDs at once, since searching
sequentially can take a long time. Using the the BioPython Entrez module
is super convenient to this end.

The results results are returned in a simple dictionary format.
"""