Introduction to Python - with application to bioinformatics
Description
Course content
This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are led through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs from scratch and to customize more complex code to fit their needs.
Format
This course runs in parallel on-site in Uppsala, Umeå and Lund. Lectures will be streamed online from one site to the other two, the host site will differ depending on who is lecturing. Several teaching assistants will be present in all three classrooms all week to help with exercises and questions. When registering you will be asked to which site you apply.
The course consists of a mix of presentations, demonstrations, and practical exercises (either in the lab with assistants or on your own). Prior to the course, you can read a companion book “Programming Python”, or “Learning Python”. Such a book will also prove useful for your programming tasks, after the course is over. It is however not required, and material will be presented in class.
Topics covered will include:
- Core concepts about Python syntax: Data types, blocks and indentation, variable scoping, iteration, functions, methods and arguments
- Different ways to control program flow using loops and conditional tests
- Regular expressions and pattern matching
- Writing functions and best-practice ways of making them usable
- Reading from and writing to files
- Code packaging and Python libraries
- How to work with biological data using external libraries.
Course fee
A course fee* of 3000 SEK for academic participants and 15000 SEK for non-academic participants will be invoiced to accepted participants. The fee includes lunches, coffee and snacks, and a course dinner.
*Please note that NBIS cannot invoice individuals
Link to registration form
Content Providers
Learning Outcomes
At the end of the course, students should be able to:
* Use variables and explain how operators work
* Process data using loops
* Separate data using if/else statements
* Use functions to read and write to files
* Describe their own approach to a coding task
* Understand the difference between functions and methods
* Be able to read the documentation for built-in functions/methods
* Give examples of use cases for dictionaries
* Write data to a simple dictionary
* Understand the concept and syntax of a function
* Write basic functions for processing data
* Describe pandas dataframes
* Give examples of how to use pandas for processing data
* Explain how regex can be used
* Define the python syntax for regex
* Combine basic concepts to create functional stand-alone programs to process data
* Write file processing Python programs that produce output to the terminal and/or external files
* Explain how to debug and further develop your skills in Python after the course
Prerequisites & Technical Requirements
Prerequisites
The course is suitable for complete beginners and assumes no prior programming experience (beyond the ability to use a text editor). A very basic knowledge of UNIX would be an advantage, such as navigating through folders and issuing commands at a shell prompt. We will not teach UNIX in detail: Other courses are available at SciLifeLab for it.
Technical requirements
Participants need to bring their own laptop with python installed for the practical exercises. A precourse session will be held to help installing the software needed.
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