• Event
  • Scientific training

Advanced Python for Biologists 2020

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:

21 September 2020

End date:

25 September 2020

Time:

09h00 - 17h00

Venue:

Earlham Institute

Registration deadline:

23 August 2020

Cost:

£550

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 is ideal for a regular python user that wishes to build upon their skills and learn more about what actually goes on behind the syntax. Martin’s teaching style is excellent and the materials were pitched at just the right level."
~ Advanced Python for Biologists course attendee, July 2019

"Excellent! The course was easy to follow but not too basic. Really well paced and Martin was very good at explaining the concepts in a relevant way."

~ Advanced Python for Biologists course attendee, July 2019


Please see here for a detailed syllabus of the course.

Course 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.

Looking for more basic training? See our Introduction to Python for Biologists 2020 course.

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.

The provisional course programme is outlined below. Please see here for a detailed syllabus of the course.

Looking for more basic training? See our Introduction to Python for Biologists 2020 course.

Day 1 - 21 September 2020

Time

Topic

09:00 - 09:30

Registration and Coffee

09:30 - 12:30

Data structures in Python
Coffee available from 10:30

12:30 - 13:30

Lunch

13:30 - 17:00

Profiling and benchmarking
Coffee available from 15:30

17:00 - 17:15

Close of Day 1

Day 2 - 22 September 2020

Time

Topic

09:00 - 09:30

Arrival coffee

09:30 - 12:30

Classes and objects

Coffee available from 10:30

12:30 - 13:30

Lunch

13:30 - 17:00

Object-oriented program design

Coffee available from 15:30

17:00 - 17:15

Close of Day 2

Day 3 - 23 September 2020

Time

Topic

09:00 - 09:30

Arrival coffee

09:30 - 12:30

Functional programming in Python

Coffee available from 10:30

12:30 - 13:30

Lunch

13:30 - 17:00

Iterators, comprehensions and generators

Coffee available from 15:30

17:00 - 17:15

Close of Day 3

Day 4 - 24 September 2020

Time

Topic

09:00 - 09:30

Arrival coffee

09:30 - 12:30

Exception handling

Coffee available from 10:30

12:30 - 13:30

Lunch

13:30 - 17:00

Unit testing

Coffee available from 15:30

17:00 - 17:15

Close of Day 4

Day 5 - 25 September 2020

Time

Topic

09:00 - 09:30

Arrival coffee

09:30 - 12:30

Programming workshop based on progress of the course and delegates' interests/problems and own data

Coffee available from 10:30

12:30 - 13:30

Lunch

13:30 - 17:00

Programming workshop based on progress of the course and delegates' interests/problems and own data (cont'd)

Coffee available from 15:30

17:00 - 17:15

Close of Day 5

  • Register today.

Registration deadline: 23 Aug 2020 - 23:45

Participation: First come, first served