Much of the popularity of Python stems from the availability of high quality libraries of existing code that we can use for our own projects. Libraries ("packages", in Python terminology) are even more useful when they are designed to work together.
For scientific programming, we are lucky to have a collection of mature packages which work together to form a stack:
- numpy for numerical processing
- pandas for reading, cleaning and processing tabular data files
- matplotlib as a low-level charting library
- seaborn as a high-level charting library for rapid dataset exploration through visualization
In this course we will learn how to use these packages together to quickly explore large biological datasets, find meaningful patterns in the data, and present our results clearly. We will focus on the high level packages - pandas and seaborn - as this will allow us to do the most work with the smallest amount of code. By concentrating on just two packages for an entire course, we will be able to cover a large part of what these tools can do.
This event will be delivered virtually via Zoom & Slack, see more details on the further information tab.
Please see here for a detailed syllabus of the course.
Who is this event for
The course is intended for anyone interested in using Python for analysis and visualization of biological datasets. Some previous experience of Python is required, as we won't cover the absolute basics of the language, so you'll need to know the very basic syntax. The introduction to Python for Biologists course gives a suitable background.
If you would like to attend the course, but have no Python experience, get in touch with Martin Jones and he will be able to suggest resources to get up to speed. If you are unsure about the suitability of this course for your needs, questions can also be directed to Martin.
This course includes plenty of practical time, including opportunities to work on your own datasets, so it might be particularly suitable for people at the start of the data analysis stage of a project.
About the trainer
Martin started his programming career by learning Perl during the course of his PhD in evolutionary biology, and started teaching other people to program soon after. Since then he has taught introductory programming to hundreds of biologists, from undergraduates to PIs, and has maintained a philosophy that programming courses must be friendly, approachable, and practical.
In his academic career, Martin mixed research and teaching at the University of Edinburgh, culminating in a two year stint as Lecturer in Bioinformatics. He now runs programming courses for biological researchers as a full time freelancer.
"Fantastic course-- excellent organisation and course content. Martin is a great teacher. Learnt a lot, especially coming from a programming-naive background.”
"This course exceeded all my expectations. Martin was a great instructor, who clearly knows how to frame any programming topic into a biology question. Now I feel very confident to keep improving my Python skills (after a couple of failed attempts with other courses in the past).”
Introduction to Python for Biologists virtual course attendees, July 2020
This training forms part of our BBSRC National Capability in Advanced Training