With your experience, what would you recommend to a wet lab, non-programmers how to learn python?

Question

[WUSCHEL]

I have a fair background in R. I would like to learn Python. However, can not find a friendly resource yet (There are too many online resources, too complex to choose!!!).

With your experience, what would you recommend to a wet lab, non-programmers how to learn python?

• I do not like Jupyter notebooks. Is any IDE for Python that friendly, like R Studio?
• What are the basics I should master?
• Any user-friendly learning materials? (how to save scripts, comments, statistics, make figures, etc)
• Any illustrated guides you can recommend?
• What is your experience learning Python as a Biologist?

[GenoMax]

Is any IDE for Python that friendly,

Visual studio code from Microsoft or PyCharm.

[Friederike]

Why would you like to learn Python? Are there specific tasks you have in mind? The resources that might be most useful to you will most likely depend on the types of applications you're hoping to do with Python.

[Dunois]

Why exactly do you want to learn/use python? If you know R you basically have almost all bioinformatics-related applications covered (at least those that a wet-lab biologist would need, anyway).

[Mensur Dlakic]

Do you speak as a regular user of both python and R? Or do you assume this to be the case?

I am primarily a python user. Last time I checked there weren't many comparable resources for deep-learning based protein modeling in R as in python. Don't think there still is an AlphaFold implementation in R. Don't think there are many R equivalents for PyTorch neural network models. That said, python is clearly behind when it comes to single-cell research, and probably in other fields that I don't know about.

[Dunois]

I am personally more a regular R user, and I only use python occasionally. My statement is mostly anecdotal plus what I've heard from the few people I've spoken to about this.

It's precisely because of the examples you raised that I used the phrase "almost all" in my comment.

Answer 1

[Mensur Dlakic]

The title of your post is misleading, and it doesn't square with what you say subsequently in the post.

I have a fair background in R.

I would give a different advice to someone who is a wet lab, non-programmer vs someone who has a fair background in R.

Separately, your question is too broad. Let's say that answering each of your bullet points is 3 sentences on average (unlikely), and someone would have to write quite an essay to answer your questions.

I will answer your last question. When I started with python, I had zero knowledge of the language. At the same time, I have been using and writing/editing program in BASIC, Fortran, Turbo Pascal and C/C++. Your R background should help, as you will soon figure out the equivalents between the two languages. For example, import in python is equivalent to library in R.

There are many IDEs for python (hint: google "python IDE"). I have tried Atom and it works well:

https://atom.io/

[Wayne]

Tagging on that...Plus, RStudio is already also an IDE for Python and the RStudio ecosystem has a lot of support built in for Python, see here, here, here, and here.
Also see here if you haven't gotten too far yet learning Python as someone who knows R.

Answer 2

[Jeremy]

Spyder, which comes with Anaconda (link below), is a good IDE.

I learned Python from the Python for Informatics class through UC San Diego Extended Studies, which is an online class that costs about 700 USD. It's good, but there's probably a cheaper way to learn Python.

Anaaconda