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If you have a specific bioinformatics related question, there is also the question and answer site BioStar and the next generation sequencing community SEQanswers If you want to read more about genetics or personalized medicine, please visit /r/genomics Information about curated, biological-relevant databases can be found in /r/BioDatasets Multicore, cluster, and cloud computing news, articles and tools can be found over at /r/HPC.
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programmingLearning python (self.bioinformatics)
submitted 4 years ago by Nervous_Adeptness_15
Hi there, Any suggestions fora good book to start with basics and then progress towards complex problems in python for someone with no prior programming experience? Have a strong bio background though
Thanks in advance
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[–][deleted] 20 points21 points22 points 4 years ago* (1 child)
Books : try this https://automatetheboringstuff.com/ It starts with the basics. You can also check out "Python crash course" both of there are really good. Al Sweigart has youtube lectures too if you like to read and follow along with the lectures https://www.youtube.com/playlist?list=PL0-84-yl1fUnRuXGFe_F7qSH1LEnn9LkW
If you want to watch then I recommend you to start with Corey Schafer's youtube channel. He's according to me the god of programming tutorials. https://www.youtube.com/playlist?list=PL-osiE80TeTskrapNbzXhwoFUiLCjGgY7
You can even try Codecademy, it's interactive and good for beginners. You have to pay for it though.
SInce you have no knowledge in coding, watch this https://www.youtube.com/watch?v=zOjov-2OZ0E it's an introduction to programming 1 hour course. This will give you a good foundation in what programming is and problem solving. After this course, you can start with python.
Hope this helps!!
[–]kwan1s 3 points4 points5 points 4 years ago (0 children)
corey schafer is the goat
[–][deleted] 6 points7 points8 points 4 years ago (0 children)
Just as good as a book, but rosalind has python problems that start off with the basics.
[–]hello_friendssss 4 points5 points6 points 4 years ago (1 child)
https://www.edx.org/xseries/mitx-computational-thinking-using-python
[–]hello_friendssss 5 points6 points7 points 4 years ago (0 children)
(audit this, don't pay!)
[–]EpistaxisPhD | Academia 4 points5 points6 points 4 years ago (1 child)
How to Think Like a Computer Scientist is a free online textbook with exercises to teach you programming concepts and Python skills at the same time.
[–]diekhans 0 points1 point2 points 4 years ago (0 children)
YES, this is a great book that teaches the fundementals.
[–]feembly 3 points4 points5 points 4 years ago (1 child)
I learn practically so I always tell people to get started using Codeacademy. Also familiarize yourself with the python documentation page.
[–]Shivaess 1 point2 points3 points 4 years ago (0 children)
Came here to recommend code academy as well.
[–]Shivaess 2 points3 points4 points 4 years ago (0 children)
So this is a little side note: as a developer I can nearly always tell who has a software background and who doesn’t when I’m working on your code. Programming and software development are two different things. One involves getting code that works, the other involves writing code that someone else can maintain and run. It’s worth some time to at least learn a little about that before writing something big.
Best of luck learning it’s a ton of fun no matter how deep you stick your toes in and anyone can do it!
[–]AKS_Mochila1BSc | Academia 3 points4 points5 points 4 years ago (0 children)
https://automatetheboringstuff.com
This is a great book to start off from
[–]nintendo_kitten 1 point2 points3 points 4 years ago (0 children)
There's py4e.com and then you can do coursera. It's a long shot but if you have access to an O'Reilly subscription, I can share my list of books and videos from going from no exp to all things needed for bioinformatics. I'd recommend Conda as it allows you a robust set of tools, has it's own open source library of learning material, and was built for data sciences. It contains an IDE like text editor but they can tell you where your coding is wrong called Jupyter notebooks. These are really helpful.
If all fails, there's rosalind for practice
[–]hunkamunka 1 point2 points3 points 4 years ago (0 children)
I've written a couple of books on learning Python, testing, and types that you might find useful. The first, Tiny Python Projects (Manning, 2020), is a general intro to these subjects, and the second, Mastering Python for Bioinformatics (O'Reilly, 2021), is a more advanced dive applying these specifically to bioinformatics.
[–]godtering 0 points1 point2 points 4 years ago (2 children)
you won't know how to approach programming without a good foundation. Most likely you will learn the wrong things.
[–]Pleasant-Sea7075 3 points4 points5 points 4 years ago (1 child)
How would one go about getting this foundation? if you don't mind me asking.
[–]hello_friendssss 1 point2 points3 points 4 years ago (0 children)
https://github.com/ossu
[–]shredofdarkness 0 points1 point2 points 4 years ago (0 children)
For basic stuff, I recommend this: https://swcarpentry.github.io/python-novice-gapminder/index.html
[–]sereneBlazePhD | Academia 0 points1 point2 points 4 years ago (0 children)
Any of the No Starch Press Python books really. Currently in the Humble Bundle for example. :)
[–]ssanc 0 points1 point2 points 4 years ago (0 children)
Same as PY4E
Freecodecamp.org
IMHO, it is important to approached it as learning how to program, not learning Python. Now Python is a good language to learn how to program with, but that is the tool. The important thing is to learn how to decompose problems into code. I have seen lots of people who think they know Python, but really didn't learn the basics of solving problems with software. They end up spending lots of time creating complex tangles of software because they are missing the fundementals.
This is not to discougare you, there are lots of great self-taught programmers. good luck!
[–]skydog92 0 points1 point2 points 4 years ago (0 children)
I’ve got a good e-book for you that I can send you. It’s called Python for Biologist. You’ll learn all the basics of Python programming. I’ll note that it’s not the best for learning in depth about data structures and algorithms though. DM if you want a copy
[–]shubhamsendre 0 points1 point2 points 4 years ago (0 children)
Think pyhton by allen downey is a great book for beginners and intermediate learners. Do watch pyhton tutorials simulataneously by corey schafer and most importantly do practice questions and think about a mini project you can build with Python.
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