Masaomi Hatakeyama
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
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 |
- 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
Python
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:
- Codecademy: Codecademy offers interactive courses that help you learn Python through hands-on practice.
- Real Python: Real Python provides in-depth tutorials and articles on various Python topics, ranging from beginner to advanced levels.
- W3Schools: W3Schools offers a comprehensive Python tutorial with examples and exercises that cover basic to advanced concepts.
- SoloLearn: SoloLearn provides a mobile app with interactive Python lessons, quizzes, and a supportive community for learning and practicing.
- Coursera: Coursera has various Python courses, including free ones, from top universities and institutions worldwide.
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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.