ch03_python.asciidoc

Chapter 3: Basics of Python programming

Python basics

This chapter introduces web sites and books for effective learning for python beginners. If you have something that is not understood in the following chapter, these information will help you.

Would like to learn Python from books

Pythonスタートブック増補改訂版:Python start book

We recommend the book if you are beginner of programming.

みんなのPython 第4版:Python for everyone

If you have any experience in programming such as Javascript and/or Java, and would like to learn python now, this book is recommended.

Would like to learn Python from any sources

Python Boot Camp(tutorial for python biginners)

This is a python tutorial event for beginner held by　PyconJP. The events held on all the places of Japan. How about join the event when it take place neighbour?

Local communities

It seems good to increase your motivation to join study workshops for beginners or for professionals. You can find many workshops in connpass site.

udemy/python

It is effective way to learn programming with online learning service but we have never tried. You should ask a reputation around. And also there are many resources in YouTube.

If you have something that is not understood in this book

py4chemoinformaticsのissues

We are happy to answer your question if you put questions in the issue of py4chemoinformatics. If there are something that is difficult to understand we will correct them. The cycle will make the document better and everybody will be happy ;)

stackoverflow

Stack Overflow is good community. You should search in SOF first and then ask the community.

Mishima.syk

Mishima.syk is the community where people who write the book gather. Topics are not limited to python but there are many presentations about python now. Discussion level is high but the community is also beginner friendly. We have planned hands-on sessions and they have an established reputation. The community members should be able to answer your questions.

Let’s use it conveniently with Jupyter notebook

By using Jupyter notebook, it is easy to write code and check the results.

The Jupyter Notebook is an open-source web application that allows you to embed code, rich text, math equation and etc. And it is easy to make high quality visualizations of the results. It is a nice platform for chemoinformatics because Jupyter Notebook can run code and draw chemical structures and many kinds of plots. Also, it has many features which improve programming productivity such as syntax highlight and auto indent. We recommend to use Jupyter especially for programming beginners.

How to use?

from terminal (in Windows, anaconda prompt)

$ jupyter notebook

After type the command above, Jupyter Notebook will be launched. In this book, all code is run on Jupyter Notebooks.

For machine learning with Python

Machine learning is a must for learning informatics not only chemoinformatics. Some background knowledge of machine learning is required in the following sessions. Scikit-learn is used for machine learning with python. Scikit-learn is de facto standard for machine learning library for python. We use the package without any descriptions but we would like to share some links for beginners.

Introduction to Machine Learning with Python

You can learn basics of machine learning with python. It is easy to read because there is less mathematical representations.

sklearn-tutorial

Sklearn tutorial hands-on by @y-sama. Written in jupyter notebook.