Wayne's Bioinformatics Code Portal fomightez

## compositioncalc1.ipynb

      
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                fomightez
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              December 20, 2015 05:19
            
              
                compositioncalc1.py from Practical Computing for Biologists by Steven H. D. Haddock and Casey W. Dunn AS A STATIC IPYTHON Notebook. Posted as a Gist by Wayne Decatur (fomightez) with full credit and reference to the original authors and note where the freely share the code online. You can see an interactive IPython gist of this at https://www.py…
              
          
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## compositioncalc1.py
# 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

## roll_ipython_in_aws.md

      
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                iamatypeofwalrus
                / roll_ipython_in_aws.md
            
            
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              January 22, 2024 11:18
            
              
                Create an iPython HTML Notebook on Amazon's AWS Free Tier from scratch.
              
          
    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


## chaossearh.py
# 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.')

## pub_med.py
#!/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))
	# 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
	# 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.')
	#!/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))