masaomi/bio334_2024

BIO334 Practical Bioinformatics

22-24, May, 2024

Masaomi Hatakeyama

• https://github.com/masaomi/bio334_2024

How to download/update this documents

Download

$ git clone https://github.com/masaomi/bio334_2024

Updating

$ git pull

Directories

• data/: input data used in some exercises
• examples/: source code of examples shown in the lecture
• jupyter_notebooks/: jupyter notebook files
• skeletons/: incompleted source code of exercises (you should fill in and complete it)
• simulation/: source code used in an advanced exercise of day2

Table of Content (Plan)

Day1
16.00-	Quick Python review bio334_day1_part1.ipynb
	Two sequences comparison bio334_day1_part2.ipynb
	Nucleotide diversity1 bio334_day1_part3.ipynb
Day2
9.00-12.00	Nucleotide diversity2 bio334_day2_part1.ipynb bio334_day2_part2.ipynb
13.00-15.00	Tajima's D calculation1 bio334_day2_part3.ipynb bio334_day2_part4.ipynb
15.00-17.00	Tajima's D calculation2 bio334_day2_part5.ipynb
Day3
9.00-12.00	Advanced exercise bio334_day3.ipynb

Exercises

• Day1 Part1: https://gist.github.com/masaomi/75ac75aa49d3603697e24864b2345d4d
• Day1 Part2: https://gist.github.com/masaomi/b2f52f4723757d5fd1b93ed422f81923
• Day1 Part3: https://gist.github.com/masaomi/857f8257e4ec9d4fb80557a5890f22a3
• Day2 Part1: https://gist.github.com/masaomi/870f24db57d295eabfd0094b504c2f1b
• Day2 Part2: https://gist.github.com/masaomi/c6c74db5ba67ff58a6b75ac195bd8143
• Day2 Part3: https://gist.github.com/masaomi/c5a11879a9deefccd40c57c1ba975b3a
• Day2 Part4: https://gist.github.com/masaomi/0f51c4a379a0b914c86c84f480e961df
• Day2 Part5: https://gist.github.com/masaomi/29c3325edd802eadb61a213140f33c93
• Day3 Final: https://gist.github.com/masaomi/1397a32c4b870f7ab7e92f479770788d
• Final exam from 2023: https://gist.github.com/masaomi/080c58eb62c40ba8b71efd9f4b45b24b

Recommended websites

Python

• Python
• Tutorial
• Glossary
• The 5 Best Websites To Learn Python Programming

General

• http://software-carpentry.org/lessons and http://www.datacarpentry.org/lessons Scientific Computing Resources for learning bash shell, programming in python, R, …]
• BioStars for questions about biocomputing and scripting for biologists
• stackoverflow for questions related to coding

Linux/Shell

• Software Carpentry tutorial - The Unix shell
• Interactive course
• Cheatsheet
• SIB e-learning: UNIX fundamentals
• Explain shell commands
• Tips & Tricks for using the shell on Mac OS
• Safe Bash scripting

and you may be able to find more sites by Google or by chatGPT...

Here are some helpful websites to learn Python:

1. Codecademy: Codecademy offers interactive courses that help you learn Python through hands-on practice.
2. Real Python: Real Python provides in-depth tutorials and articles on various Python topics, ranging from beginner to advanced levels.
3. W3Schools: W3Schools offers a comprehensive Python tutorial with examples and exercises that cover basic to advanced concepts.
4. SoloLearn: SoloLearn provides a mobile app with interactive Python lessons, quizzes, and a supportive community for learning and practicing.
5. Coursera: Coursera has various Python courses, including free ones, from top universities and institutions worldwide.
6. edX: edX also offers Python courses from top universities, and you can audit many of them for free.

These websites offer various resources to help you learn Python at your own pace. Don't hesitate to explore them and find the one that best suits your learning style.