Python for biologists resources
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(Note from Lenny Teytelman)
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Back in 2007, I co-organized a "Intro Programming for Bioinformatics" bootcamp at Berkeley. I was inspired by Lincoln Stein's CSHL course "Programming for Biologists."
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I strongly belive that biologists should spend some time learning to code. It's not hard. Won't make you a computation biologist who develops the better BLAST, but it will make you a better and more capable scientist.
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Taking a computer science class or a quick course is terrific. But not everyone can do that, so I just asked on Twitter for online recommendations.
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Below are the many great recommendations. Please add others to this list!
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Recommendation (online tutorials)Suggested ByTweetComments
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intro-prog-bioinfo-2014.wikispaces.com@lteytelmanhttps://twitter.com/lteytelman/status/616270947201368064
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http://programmingforbiology.org/@hyphaltiphttps://twitter.com/hyphaltip/status/616316136041267200
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http://learnpythonthehardway.org/ @sciliz and @usethespacebarhttps://twitter.com/usethespacebar/status/616274529720082432Endorsed by many
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http://people.duke.edu/~ccc14/sta-663/IntroductionToPython.html@usethespacebarhttps://twitter.com/usethespacebar/status/616287911814803456
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http://software-carpentry.org/lessons.html@nextgenseekhttps://twitter.com/nextgenseek/status/616293314153721856Endorsed by many
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https://developers.google.com/edu/python/@Asif_Mehedihttps://twitter.com/Asif_Mehedi/status/616303440327741442
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https://www.udacity.com/course/programming-foundations-with-python--ud036@TrishWhetzelhttps://twitter.com/TrishWhetzel/status/616306929451675648Endorsed by many
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https://www.coursera.org/course/pythonlearn@NazeefaFatimahttps://twitter.com/NazeefaFatima/status/616278430619975680Endorsed by many
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https://github.com/sjspielman/UTbiocomputing2015@WrightingAprilhttps://twitter.com/WrightingApril/status/616271916085587968
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http://cli.learncodethehardway.org/book/@JamesPBLloydhttps://twitter.com/JamesPBLloyd/status/616283009675755521unix
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http://rosalind.info/problems/locations/@madbugsciencehttps://twitter.com/madbugscience/status/616282805492953088
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http://www.programmingforbiologists.org/@anthonygitterhttps://twitter.com/anthonygitter/status/616279490252115968
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http://www.acgt.me/blog/2015/6/22/command-line-bootcamp-learn-the-basics-of-unix@anthonygitterhttps://twitter.com/MicroWavesSci/status/616271710388666368unix
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http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-00sc-introduction-to-computer-science-and-programming-spring-2011/
@anthonygitterhttps://twitter.com/rkrishnasanka/status/616370707132477440
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http://interactivepython.org/courselib/static/thinkcspy/index.html@schwessinger
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http://pythonforbiologists.com/
@davelunt and @JamesPBLloyd
https://twitter.com/JamesPBLloyd/status/616283009675755521See also @pythonforbiolog
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http://exercism.io@markjmandelhttps://twitter.com/markjmandel/status/617153732502028288Other languages too
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https://www.youtube.com/playlist?list=PLesCEcYj003QxPQ4vTXkt22-E11aQvoVj
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http://readiab.org/@TomSilico / @combine_auhttps://twitter.com/TomSilico/status/618547798644883456
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Books
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http://www.nostarch.com/pythoncrashcourse@bfwriterhttps://twitter.com/bfwriter/status/616307621298053124https://twitter.com/bfwriter/status/616307560308719616
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http://www.amazon.com/Bioinformatics-Data-Skills-Reproducible-Research/dp/1449367372@pjacockhttps://twitter.com/pjacock/status/616296978343940100
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http://www.amazon.com/Practical-Computing-Biologists-Steven-Haddock/dp/0878933913@JamesPBLloydhttps://twitter.com/JamesPBLloyd/status/616283009675755521
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@arvestadhttps://twitter.com/arvestad/status/616316142626447361
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http://www.amazon.co.uk/Advanced-Python-Biologists-Martin-Jones/dp/1495244377@biomickwatson
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http://interactivepython.org/courselib/static/thinkcspy/index.html@schwessinger
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http://www.amazon.com/Python-Programming-Introduction-Computer-Science/dp/1887902996@teralevinhttps://twitter.com/tera_levin/status/616666753251287041Great intro to computer science concepts too
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http://www.amazon.com/Beginning-Python-From-Novice-Professional/dp/159059519X@alanrrogershttps://twitter.com/alanrrogers/status/616764105936867328
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http://www.greenteapress.com/thinkpython/html/@lesabot
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Libraries and other
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https://github.com/svaksha/pythonidae@usethespacebarhttps://twitter.com/usethespacebar/status/616275255598927873
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https://github.com/hyphaltip/CSHL_NGS@hyphaltiphttps://twitter.com/hyphaltip/status/616316136041267200NGS Slides and Examples
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http://www.pyvideo.org/@Asif_Mehedihttps://twitter.com/Asif_Mehedi/status/616303579788394496videos
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http://www.codecademy.com/@ZLeeilyhttps://twitter.com/ZLeeily/status/616284064203571200https://twitter.com/Bashir9ist/status/616283833562959872Endorsed by many
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https://www.reddit.com/r/learnpython@brouberolhttps://twitter.com/brouberol/status/616343623899213824
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http://coderscrowd.com/app/public/home@radanibahttps://twitter.com/radaniba/status/616302224981921792
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http://perthon.sourceforge.net/@thesciencewebConvert python into perl
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Lists of resources
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https://docs.google.com/spreadsheets/d/1J8Ee8Vy4dv5wHWDAg4K9yb_ID5qvw4LaDOZEt4QKm60/edit#gid=0
@jeffk8900https://twitter.com/jeffk8900/status/616280871708983296whatsi
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Web Based Interactive Resources To Learn Programming And/Or Bioinformatics@NazeefaFatimahttps://twitter.com/NazeefaFatima/status/616278430619975680
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Installers and Package Managers
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https://store.continuum.io/cshop/anaconda/@hoffsbeefshttps://store.continuum.io/cshop/anaconda/
Distribution manager for scientific python: easy and flexible for non root users!
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Python for the modern biodata scientist (includes conda directions)@dhimmelhttps://twitter.com/dhimmel/status/616292874070523904
Describes managing separate 2 and 3 conda environments
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Enthought Canopy Academic@warpcorebreach
convenient python distribution, free for academics
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