• Event
  • Scientific training

Advanced Python for Biologists 2021

This Advanced level workshop is ideal for researchers and technical workers with a background in biology and a basic knowledge of Python, to develop bigger or more complicated programs and increase skills and knowledge about the language, including object-oriented approaches to programming.

Start date:

04 October 2021

End date:

15 October 2021

Time:

09h00 - 12h30

Venue:

Online (via Zoom)

Registration deadline:

05 September 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 people who already have a basic knowledge of Python and are interested in using the language to tackle larger problems. In it, we will look in detail at the parts of the language which are particularly useful in scientific programming, and at the tools Python offers for making development faster and easier.

The workshop will use examples and exercises drawn from various aspects of bioinformatics work. After completing the workshop, students should be in a position to -

(1) take advantage of the advanced language features in their own programs and

(2) use appropriate tools when developing software programs.

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.

“Martin is an excellent teacher--coming from a non-programing background, I have enjoyed being on his Python courses and inspired to pursue programming beyond my PhD.”

“Don't hesitate to sign up if you're intimidated by the "Advanced" course title. Martin goes at such a clear pace that you'll be accommodated as long as you have any familiarity with coding and an awareness of Python's basic functions.”

- Advanced Python for Biologists virtual course attendees, October 2020

Who is this event for

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) and should also have basic Python experience. Students should be familiar with the use of lists, loops, functions and conditions in Python and have written at least a few small programs from scratch.

This course is aimed at people who want to develop bigger or more complicated programs in Python, or to learn more about the language, or to explore different approaches (object-oriented, functional) to programming. The material covered is very general purpose and can be applied to any kind of problem.

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 - 04 October 2021

Time

Topic

09:30 - 12:30

Data Structures in Python

Day 2 - 05 October 2021

Time

Topic

09:30 - 12:30

Profiling and Benchmarking

Day 3 - 06 October 2021

Time

Topic

09:30 - 12:30

Classes and Objects

Day 4 - 07 October 2021

Time

Topic

09:30 - 12:30

Object-oriented Program Design

Day 5 - 08 October 2021

Time

Topic

09:30 - 12:30

Functional Programming in Python

Day 6 - 11 October 2021

Time

Topic

09:30 - 12:30

Iterators, Comprehensions and Generators

Day 7 - 12 October 2021

Time

Topic

09:30 - 12:30

Exception Handling

Day 8 - 13 October 2021

Time

Topic

09:30 - 12:30

Unit Testing

Day 9 - 14 October 2021

Time

Topic

09:30 - 12:30

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

Day 10 - 15 October 2021

Time

Topic

09:30 - 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 4 October – Friday 15 October 2021, weekdays only. 
  • On 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

  • Register today.

Registration deadline: 5 Sep 2021 - 23:45

Participation: First come, first served