TOPIC: Python
If the user is interested in natively installing python on their computer, please see https://www.python.org/downloads/
Otherwise, see: Introduction to using Jupiter notebooks via MyBinder.org
Python is rapidly becoming the preferred coding language of data scientists and bioinformaticians because it is easy to interpret and debug. Python’s built in data structures also allows for more concise codes compared to languages like Java and C++. Plus, it has been more broadly applicable than other languages such as R that is traditionally targeted at statistical computing and graphics. It is not surprising that many bioinformatics pipelines have Python components and numerous bioinformatics tools/tool compilations are python-based. By becoming fluent in Python, a user with raw genomics, field measurements, or structural data can do everything from raw data processing to processed data cleanup/ sorting, statistics, machine learning, data visualization and sharing the results via a Python-based web framework. Additionally, one can use Python skills to program drones and sensors to collect data from a large range of experimental sources.
The goal of this module is to give the participant experience using Python in ways relevant to bioinformatics through collaborating on a project. For participants that are not experienced in Python, we recommend working through the provided tutorials covering the basics (syntax, data structures, basic sorting and searching, data import/export) before moving on to the project-based learning exercises.
This topic will cover:
Basic:
- Python syntax and data structures
- Data sorting and manipulation
- Functions- by the user and from widely used libraries
Advanced:
- Python Pandas dataframes
- Directory/batch file methods
- Statistics/Data reduction
- Biopython
Lessons can be found at the following repository
Date posted: 14 April 2020
Author(s): Dr. Ashley B. Cohen
Instructor(s): Dr. Ashley B. Cohen
- Exploring the features of Binder
- Running a simple script
- Typing python commands in a terminal environment
Date posted: 14 April 2020
Author(s): Dr. Ashley B. Cohen
Instructor(s): Dr. Ashley B. Cohen
Content | Video presentation |
Date posted: 30 April 2020
Author(s): Dr. Ben Tully
Instructor(s): Dr. Ben Tully
- Set and determine the datatype of a variable using python methods
- Apply some of the built-in python string functions to manipulate the way that text is displayed in print statements
Date posted: 30 April 2020
Author(s): Dr. Ben Tully
Instructor(s): Dr. Ben Tully
Content |
TBD
TBD
TBD
Tools:
- https://biopython.org
- https://www.shogun-toolbox.org
- https://keras.io
- https://scikit-learn.org/stable/
Basic:
- https://www.pythonforbeginners.com/
- https://docs.python.org/3/tutorial/
- https://docs.scipy.org/doc/numpy/user/quickstart.html
- https://software-carpentry.org/lessons/
Advanced: