Introduction and software installation

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Why I need to learn programming?

Biological big data become a potent method for clinical and biomedical research

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Data-driven VS Hypothesis driven

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Programming language

• Python (https://www.python.org/)
• R (https://www.r-project.org/)
• Perl (https://www.perl.org/)
• C/C++
• Ruby (https://www.ruby-lang.org)
• Java (https://www.java.com/)
• C#
• PHP (https://www.php.net/)
• HTML
• Bash shall script

Bioinformatics

Omics

Object oriented, GUI

Web-based

Unix script

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Syllabus

• TA: Jonathan Lin (林炘叡)
• The score will be evaluated based on the final project.
• The correctness: 70%
• The code: 30%
• You can go to 國IR 5034 for the demonstration anytime. And please bring or send your scripts to us after the demonstration.
• Deadline: 2023/06/21

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Where to get the videos and slides

• https://sung-huan.github.io/course.html

• Due the limitation of storage, please download the files within one week (after the course).

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VSCODE

• https://code.visualstudio.com/

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Python installed via anaconda

https://www.anaconda.com/download/success

Select it

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Install extension

• Install python and pylance

Edit region

Terminal

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Select Conda one

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Python installed by standalone (if anaconda does not work)

• https://www.python.org/downloads/
• Download the latest version

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Set executable path

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A simple testing code – your first python script

• In the edit region type print(“Hello world”)
• Save it to be a python script (suffix .py)
• Run the script by Ctrl+F5 or F5
• Normally, you can also run the script at the terminal by typing python test.py or python3 test.py
• If you cannot get the output, you should set the environmental PATH.

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Set environmental PATH

1. Go to “system” and select 進階系統設定

2. Select 環境變數

3. Edit the environmental path

3. Copy the path of

python folder, not

exe file. Then paste

It to the block of

environmental path

5. Python path should be added.

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How about Mac or Linux?

• Mac and Linux are both unix based system. They all have installed python by default.
• VS code has Linux and Mac version can be downloaded.
• Please follow the same procedure to setup extension and python path for VS code.

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Further suggestions to Mac users

• Install Homebrew (https://brew.sh/index_zh-tw)
• Open your terminal (normally is shown as a button below).
• Type the command

​

• Then type

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• A program called pip3 will be installed as well. It can install python package automatically and conveniently.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

/brew install python3

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Further suggestions to Linux users

• If you have no python3 (sometimes Linux has only installed python2), open your terminal and type sudo apt-get install python3.10 (3.10 is the version number. It can be changed.)
• Open your terminal and type sudo apt-get install python3-pip
• pip3 will be installed as well.

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�Useful websites and forums

• PyPI (https://pypi.org/)
• Collection of python packages
• A similar collection for R is Bioconductor (https://www.bioconductor.org/)
• GitHub (https://github.com/)
• Platform for code or resource sharing, exchanging and storing
• Docker (https://www.docker.com/) or DockerHub (https://hub.docker.com/)
• A software and collector for installing and distributing software with environmental setting
• Stack overflow (https://stackoverflow.com/)
• A useful forum for asking and answering questions

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Other software

• Anaconda (https://www.anaconda.com/products/distribution)
• An all-inclusive python package collectors
• Sublime (https://www.sublimetext.com/)
• A software for managing and edit python scripts and packages.
• Kite (https://www.kite.com/)
• An AI coding assistant
• Pycharm (https://www.jetbrains.com/pycharm/)
• A python manager and editor
• Pylint (https://pylint.pycqa.org/en/latest/)
• Evaluating the quality and style of python scripts.
• Biopython (https://biopython.org/)
• A package for bioinformatics

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