Thank you to all that contributed to my request for Python resources. Here is a compilation of the responses. Thank you once again, Michael. I'm sure someone else will mention this, but: http://rosalind.info/problems/locations/ "Rosalind is a platform for learning bioinformatics through problem solving." Have fun! Cheers, Anders Dear Michael, I suggest to start with codecademy: http://www.codecademy.com/ It's good to learn the basics, and then move to BioPython. cheers, Andrea This is good…learn through doing: http://rosalind.info/problems/locations/ Less directly relevant but might be of interest: https://www.coursera.org/course/bioinformatics https://beta.stepic.org/Bioinformatics-Algorithms-2/ Dear Michael I recommend: If you are in a hurry: http://www.amazon.co.uk/Python-Bioinformatics-Bartlett-Biomedical-Informatics/dp/0763751863/ref=sr_1_2?ie=UTF8&qid=1381273389&sr=8-2&keywords=python+bioinformatics If you are NOT in a hurry, I have been reviewing a new book coming out in December that looks better: 'Managing Your Biological Data with Python' by Allegra Via et al. (CRC Press) The Coursera MOOC course (not a book) is nice, and the Rosalind people wrote chapter 1 there https://www.coursera.org/course/bioinformatics https://beta.stepic.org/Where-Does-DNA-Replication-Begin-2/ Best of luck. Please let me know if thisis useful Pedro Fernandes Dear Michael, I used Practical Computing for Biologists, by Haddock and Dunn, to introduce myself to Python programming (with no prior experience) and I highly recommend it. Good luck in your search! Best, Abby Dear Micheal, I am also interested in learning Python, and registered a course in COURSERA (but I was busy and couldn't make it). There is another course started this week on Python: https://www.coursera.org/course/interactivepython, if you are interested in. I attached some sources from the sources of the last course: Some in-depth free python 3 ebooks: Dive Into Python 3 A Byte of Python Think Python: How to Think Like a Computer Scientist Think Complexity (possibly a bit too high-level for LTP class) Invent Your Own Computer Games with Python 2nd Edition Free Python Books Free online courses to help you learn Python: Google's Python Class Learn Python the hard way (HTML Format) Codecademy: Python I hope these are of your interest. Cheers, Abdy University of Helsinki I learned a ton from Practical Computing for Biologists by Haddock & Dunn. Clear, logical, thorough. Also has shell scripting, using text editors effectively, relational databases and remote computing. Cheers, Sara A few years back I co-taught a course on Python for bioinformatics. We used _Learning Python_ by Lutz. I currently have the 3rd edition which is most up to date but has too much stuff in it and is not as beginner- friendly as the second edition. The powerpoint for our class is at: http://homes.cs.washington.edu/~ruzzo/courses/gs559/09wi/ (if you can see that from outside UW--I'm not certain, sorry). Hope this helps. I didn't speak Python before starting to teach this class and found it fairly easy to pick up (one step ahead of the students) but I'm an experienced programmer. Mary Kuhner mkkuhner@uw.edu Hi Micheal Can you please post the responses you get? I have used a couple of online sources. I really liked CodeAcademy and there is also a great YouTube video if you are a complete beginner. http://youtu.be/N-ae8Q_7iCA I also notice that google has some Python tutorial videos on YouTube but I haven't checked those out yet. The book that was recommended to me is Practical Computing for Biologist by Haddock and Dunn. Cheers, Rachel Closito, Ph.D. Biology Department University of Louisiana at Lafayette We have been using python for biologists: http://pythonforbiologists.com/index.php/introduction-to-python-for-biologists/ Nicola Anthony Associate Professor Department of Biological Sciences University of New Orleans New Orleans LA 70148 USA Hi Michael, I used udacity to learn python. See http://abetterscientist.wordpress.com/2012/10/16/being-a-better-programmer-learning-python-with-udacity/ Best, Pleuni "Practical Computing for Biologists" by S. Haddock & C. Dunn ------- Maggie R. Wagner Ph.D. Candidate Department of Biology Program in Genetics & Genomics Duke University Dear Micheal, This is what I used and had other students teach themselves with. I hope it helps! Best, Ann Kathrin I recommend this book: http://practicalcomputing.org/ It has some very useful python chapters. It is also aimed at biologists Ian Hi Michael, I have been learning python with: Bioinformatics Programming using Python by Mitchell L. Model (O'Reilly). Personally, I think it's a very good book. This has been my first experience with learning a scripting language and I've found the book very helpful. Hope this helps, Cornelya Dear Michael, Haddock and Dunn’s Practical Computing for Biologists, Sinauer 20111 is a good place to start. Sincerely, Dr. Joseph L. Graves Jr. Associate Dean for Research Joint School of Nanoscience & Nanoengineering NCATSU & UNC Greensboro 2907 E. Lee St. Greensboro, NC 27401 Phone: 336-285-2858 Mobile: 336-707-1556 Fax: 336-334-5179 http://jsnn.ncat.uncg.edu/ Dear Michael, I am just starting on this myself. If you get good recommendations I would love to hear them. So far I just have the typical access to stuff like: http://www.learnpython.org/ general basics and then the links on Biopython pages http://biopython.org/wiki/Category:Wiki_Documentation otherwise am just looking for specific minicourses online and seeing i I can download course materials... Have you seen ROSALIND? http://rosalind.info/problems/locations/ Danna Dear Michael, I am a Biologist and in the last few months I learned to write basic scripts from scratch! This made my analysis routine a lot faster and easier! I started with the book Haddock, SHD and CW Dunn (2011) Practical Computing for Biologists. Sinauer Associates (Sunderland, MA). But I found the coursera (www.coursera.org) courses on Python ("Learn to Program: The Fundamentals and Learn to Program: Crafting quality code") really helpful!!! I highly recommend them! After I learned the basic syntax of the language then google was the biggest help! Best of luck, Paschalia Kapli Dear Michael, I’ve just spent the last summer learning python for a bioinformatic context. The books I found the most useful are actually free: For general Python: “How to think like a computer scientist” http://www.greenteapress.com/thinkpython/thinkpython.html and Bioninformatics specific: “BioPython” http://biopython.org/DIST/docs/tutorial/Tutorial.pdf In addition, many of the python bioninformatics modules have pretty good documentation online: e.g. PyVcf: http://pyvcf.readthedocs.org/en/latest/ Hope this helps, Cheers, Axel Hi Michael, You should take a look at http://www.codecademy.com (general interactive Python tutorial, great for learning syntax), and http://rosalind.info (has general Python tutorial and bioinformatics specific challenges). Cheers, Krisztina Rigo hi, this coursera course should be a very good option: https://www.coursera.org/course/interactivepython coursera partners with top universities to offer great courses online for free. this one just started yesterday, so you're perfectly on time to enrol. I haven't taken that one, but I have taken some other coursera courses, and they're great! free education for everybody! I hope that helps. bes,t, david Hello Michael, I highly suggest two resources, the first one is codecademy, not biologically oriented but a good start two learn the basis of python. The second obe is rosalind, it´s a learning platform oriented through problem solving to help learn bio-informatics. You can use other languages than python bir it´s really interesting and challenging. Best, Philippe Envoyé de mon iPhone Hello Michael, you might want to look into this online COURSERA course: https://www.coursera.org/#course/interactivepython started yesterday. Best, Tom Bochynek Michael McLeish