Introduction to Programming for Bioinformatics using Python and R.

• Lecturer: Gang Chen ([email protected])
• Laptop is required for this courses
• Most softwares and packages in this courses are available on Windows, Linux and Mac OS. However, Linux and Mac OS are recommended for Bioinformatics.
• All slides of this courses are written in Markdown or LaTeX. You can check out source codes of these slides from GitHub.

Date: 10 Sept 2016

• Computer Architecture
• Computer Network

• CS301: COMPUTER ARCHITECTURE

Date: 17 Sept 2016

• Overview of Python
• Setting Up Python Development Environment
• Hello Python
• Interactive and Script mode

• A IPython Notebook for Introduction to Python also can be used as a reference for 3rd week.
• Python Courses on codecademy an interactive courses of Python for people who don't have any programming experiences.
• A byte of Python
• The Hitchhiker’s Guide to Python

24 Sept 2016

• Data Type
• Variable
• List and map
• Flow Control: conditional statement and loop
• Function and module

• Computational Complexity Theory from Stanford University
• Introduction to Algorithms, 2nd
• Algorithms, 4th

8 Oct 2016

See references of Lecture 2.

15 Oct 2016

See references of Lecture 2.

22 Oct 2016

• Web Development Overview
  • Overview
  • LAMP: Operation System, Web Server, Database, Programming language
  • LAMP: HTML, CSS, Javascript, Python, SQL
  • A static website
• CGI
• Connect CGI to Database
• Web Framework: Django
• A online sequence aligner

• Django Documentations

Date: 29 Oct 2016

• NumPy, SciPy, Pandas: Scientific computing
• Scikit-Learn, NLTK: Machine Learning and natural language processing
• Matplotlib: Data visualization in Python

• Machine Learning Exercises In Python

Exercises in Python for Andrew Ng's Machine Learning courses.

• Building Machine Learning Systems with Python

5 Nov 2016

• Bioinformatics Programming using Python

12 Nov 2016

• R in Action, 2nd

19 Nov 2016

• BioConductor
• Workflow of RNA-Seq data analysis
• Visualization of Biological Data

26 Nov 2016

• The Code Complete 2nd

3 Dec 2016

10 Dec 2016

Review slides and assignments.