• Event
  • Scientific training

Introduction to Python for Biologists 2021

This introductory level course is intended for people with a biological background but with no previous programming experience. The course introduces basic programming concepts with plenty of time to practice writing code and working on your own data.

Start date:

05 July 2021

End date:

16 July 2021

Time:

09h00 - 12h30

Venue:

Online (via Zoom)

Registration deadline:

27 June 2021

Cost:

£450

About the event.

About the event

Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience.

It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions.

After completing the workshop, students should be in a position to -

(1) apply the skills they have learned to tackling problems in their own research and

(2) continue their Python education in a self-directed way.

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.

"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

Who is this event for

This workshop is aimed at researchers and technical workers with a background in biology, but no previous programming experience.

Students should have enough biological/bioinformatics background to appreciate the examples and exercise problems (i.e. they should know what a protein accession number, BLAST report, and FASTA sequence is). The syllabus has been planned with complete beginners to programming in mind, so no particular computer skills (beyond the ability to use a text editor) are necessary.

If you are unsure about the suitability of this course for your needs, questions can be directed to Martin Jones.

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.

Programme.

 

Day 1 - 05 July 2021

Time

Topic

09:00 - 12:30

Introduction & Manipulating text

Day 2 - 06 July 2021

Time

Topic

09:00 - 12:30

Working with Files

Day 3 - 07 July 2021

Time

Topic

09:00 - 12:30

Lists and loops

Day 4 - 08 July 2021

Time

Topic

09:00 - 12:30

Conditions

Day 5 - 09 July 2021

Time

Topic

09:00 - 12:30

Writing functions

Day 6 - 12 July 2021

Time

Topic

09:00 - 12:30

Regular expressions

Day 7 - 13 July 2021

Time

Topic

09:00 - 12:30

Dictionaries

Day 8 - 14 July 2021

Time

Topic

09:00 - 12:30

Working with the file system

Day 9 - 15 July 2021

Time

Topic

09:00 - 12:30

Programming workshop based on progress of the course and delegates’ interests

Day 10 - 16 July 2021

Time

Topic

09:00 - 12:30

Programming workshop based on progress of the course and delegates’ interests

Further information.

This event will be delivered virtually, in the following format:

  • The programme will be delivered over ten days, from Monday 5 - Friday 16 July 2021, weekday mornings only.
  • Each day there will be 3.5 hours of live input (via Zoom) from the trainer (9:00-12:30 UK/GMT+1, including breaks).
  • Training will consist of lectures, demonstrations and practical exercises, with the trainer on hand to assist and offer 1-1 support.
  • Slack will be used to share important updates and for asking questions
  • Lectures/input will be recorded and made available to participants as soon as possible for anyone who needs to catch up.
  • You will need to have an account for Zoom and Slack. We recommend that you download the clients for these rather than using the browser version. 

Hardware

To follow along with the live programming examples you'll need to be able to have two windows open - one for the zoom video, and one for your own code. The best way to do this is to either have a single large monitor, or two small ones. If you're using a laptop, an external monitor is a good idea. Working on just a single laptop screen is possible, but it will involve a lot of switching between windows. Remember that your zoom window will need to be big enough for you to see code, so a small window that works fine for chatting will probably not be big enough.

Software

To run the Python code and follow the interactive notebooks, you'll need to download and install Anaconda from this link: https://www.anaconda.com/products/individual

Make sure you get the right installer for your operating system (Windows, Mac or Linux) and make sure you get the Python 3.7 version. Please install this even if you already have a version of Python on your system, as we will need to be all running the same environment for the course to go smoothly. 

The Anaconda package takes a while to download and install, so please do this well in advance of the course and get in touch if you have problems - don't leave it until the last minute. We won't have time during the class to stop and troubleshoot problems with your installation, but we can help you get it set up in advance.

 

Terms and conditions

Please carefully review our standard online event booking terms and conditions prior to registering for this event. Completing an online registration and associated payment process will mean that you are bound by these terms and conditions. Any supplemental terms or changes to these conditions on a per event basis will be included on this page. If you have any queries regarding our events or in relation to your booking, please contact us at training@earlham.ac.uk