• Event
  • Scientific training

Advanced Python for Biologists

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:

22 July 2019

End date:

26 July 2019

Time:

09h00 - 17h00

Venue:

Earlham Institute

Registration deadline:

16 June 2019

Cost:

£600

About the event.

What is the workshop about?

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.

What will I learn?

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.

Prerequisites:

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.

During the workshop students will use their own laptops. Instructions for any software to be installed will be sent out prior to the course.

Target audience:

This workshop is aimed at researchers and technical workers with a background in biology and a basic knowledge of Python.

The Advanced 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.

If time permits and it is of interest to the delegates, the final sessions on the last day of the course will also cover data visualisation tools. 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 - 22 July 2019

Time

Topic

09:00 - 09:30

Registration and Coffee

09:30 - 12:30

Efficient use of data structures

Coffee available from 10:30am

12:30 - 13:30

Lunch

13:30 - 17:00

Exception handling

Coffee available from 15:30pm

17:00 - 17:15

Close of Day 1

Day 2 - 23 July 2019

Time

Topic

09:00 - 09:30

Arrival coffee

09:30 - 12:30

Classes and Objects

Coffee available from 10:30am

12:30 - 13:30

Lunch

13:30 - 17:00

Object oriented program design

Coffee available from 15:30pm

17:00 - 17:15

Close of Day 2

Day 3 - 24 July 2019

Time

Topic

09:00 - 09:30

Arrival coffee

09:30 - 12:30

Functional programming in Python

Coffee available from 10:30am

12:30 - 13:30

Lunch

13:30 - 17:00

Iterators, comprehensions and generators

Coffee available from 15:30pm

17:00 - 17:15

Close of Day 3

Day 4 - 25 July 2019

Time

Topic

09:00 - 09:30

Arrival coffee

09:30 - 12:30

Performance and benchmarking

Coffee available from 10:30am

12:30 - 13:30

Lunch

13:30 - 17:00

Unit testing and robust code

Coffee available from 15:30pm

17:00 - 17:15

Close of Day 4

Day 5 - 26 July 2019

Time

Topic

09:00 - 09:30

Arrival coffee

09:30 - 12:30

Programming workshop based on delegates' interests

Coffee available from 10:30am

12:30 - 13:30

Lunch

13:30 - 17:00

Programming workshop based on delegates' interests

Coffee available from 15:30pm

17:00 - 17:15

Close of Day 5

Fees and accommodation.

Registration includes lunch and refreshments.

Accommodation is not included, however we are pleased to provide links to a couple of options which we have used in the past:

UEA’s Broadview Lodge provides en-suite, student-style accommodation at a cost of approximately £55 per night (board only) and is approximately 20 minutes walk to the institute.

For somewhere more central the Maid’s Head Hotel offers bed and breakfast at approximately £120 per night single occupancy, and is approximately 20-30 minute taxi ride from the institute.

  • Register today.

Registration deadline: 16 June 2019

Participation: First come, first served