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UAI 655 Python and Bash course for bioinformatics beginners

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Marta Vohnoutova edited this page Mar 15, 2017 · 5 revisions
  1. Welcome to the UAI-655-Python-and-Bash wiki!
This is a course UAI 655 Python and Bash course for bioinformatics - beginners. The pages you can read or download study material is here [UAI](https://github.com/MartaVohnoutovaBukovec/IOS-655-Python-a-Bash/tree/master/IOS%20655%20Python%20a%20Bash/diveintopython3-master). The course is for informatics - beginners. It will last one semester and **ends with the credit and the exam**. It will be presented all in english. For the credit, the students must submit homeworks and 80% participance. The course will be held every Friday (almost - 24.2 and 3.3. I cannot come) 10.30 - 14.30. 
- We must agree on spare lectures.
    • The environment**
    • Sit and login all the time to the same computer**
  • virtual environment - right upper corner
  • click UAI Ubuntu / blue icon
  • Linux Ubuntu 16.04 64bit
  • Python 3.5.2
  • Internet access
  • user user
  • password Aa123456
    • Recommended literature**
  • dive-into-python3_engl
  • book.programming_in_python_3.summerfield.pdf - this is a teaching book
Next semester we will continue with **biopython**
  • Cambridge.University.Python.Apr.2015.ISBN.0521895839.pdf
  • Tutorial Biopython.pdf
Examples and training files will be in [IOS](https://github.com/MartaVohnoutovaBukovec/IOS-655-Python-a-Bash/tree/master/IOS%20655%20Python%20a%20Bash/diveintopython3-master/examples).
    • Organization of the course**
We have only several listener, so lectures and training are combine, ask any time. Break after every 60 minutes app. Because the name of the course is "Bash" and it is in the linux environment: ![Basic](https://github.com/MartaVohnoutovaBukovec/IOS-655-Python-a-Bash/blob/master/IOS%20655%20Python%20a%20Bash/diveintopython3-master/examples/Python%20Cheatsheet%20-%20Cyberpunk%20University.jpg)
    • Course content**
  • [Linux](https://github.com/MartaVohnoutovaBukovec/IOS-655-Python-a-Bash/wiki/UAI-655---Linux-command-line)
  • Python installation
  • Chapter 1. Rapid Introduction to Procedural Programming
  • Chapter 2. Data Types
  • Chapter 3. Collection Data Types
  • Chapter 4. Control Structures and Functions
  • Chapter 5. Modules
  • Chapter 6. Object-Oriented Programming
  • Chapter 7. File Handling
  • Chapter 8. Advanced Programming Techniques
  • Chapter 9. Debugging, Testing, and Profiling
  • Chapter 10. Processes and Threading
  • Chapter 11. Networking
  • Chapter 12. Database Programming
  • Chapter 13. Regular Expressions
  • Chapter 14. Introduction to Parsing
  • Chapter 15. Introduction to GUI Programming

Link to Python documentation and basics tutorial - https://docs.python.org/3.10/tutorial/index.html

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