Training

I regularly teach instructor-led training courses, mostly in Python and with an emphasis on practical problem-solving.

“The course was really well pitched for someone with very little informatics background … learning from a biologist is so much better than learning from an informatics person, because you already know what we do and don’t know and understand, and all the examples used situations which we could intuitively grasp straight away. Thank you very much for an excellent week which will change the way I work from now on.” -Ellen, King’s College London

If you’re reading this this website and think you might benefit from an instructor-led programming course, then there are probably a bunch of other people in your organization who feel the same way, so drop me an email at martin@pythonforbiologists.com and I’ll arrange to chat with you. I specialize in teaching complete beginners, and have most experience with teaching programming for biological analysis. In the past I’ve run week-long introductory courses and advanced courses, along with shorter courses targeting specific areas of programming (E.g. functional Python, object-oriented Python). However, if you have something else in mind, don’t hesitate to ask – I have a strong interest in teaching programming as a tool for workers in all types of data-heavy environments.

You might be interested to read my thoughts on the role of instructors in programming training.


 

Upcoming courses

Introduction to Python for Biologists

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.

 

Monday 27th February to Friday 3rd March at the Centre for Genome Enabled Biology and Medicine in Aberdeen, Scotland. Click here for details and to register.

Monday 10th to Friday 14th April 2017 at Edinburgh Genomics in Edinburgh, Scotland – Click here for details and to register.

 

Biological data visualization and manipulation in Python

One of the strengths of the Python language is the availability of mature, high­ quality libraries for working with scientific data. Integration between the most popular libraries has lead to the concept of a “scientific Python stack”: a collection of packages which are designed to work well together. In this workshop we will see how to leverage these libraries to efficiently work with and visualize large volumes of data.

Monday 13th to Friday 17th March 2017 at Physalia Courses in Berlin, Germany. Click here for details and to register.

Monday 10th to Friday 14th July 2017 at Edinburgh Genomics in Edinburgh, Scotland. Click here for details and to register.

Monday 4th to Friday 8th December 2017 at Margham in Wales with PR Statistics. Click here for  details and to register.

 

Introduction to Linux and workflows for biologists

Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customize their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data.

Monday 24th to Friday 28th April 2017 at Edinburgh Genomics in Edinburgh, Scotland. Click here for details and to register.

 

Advanced Python for Biologists

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 course 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.

Monday 6th to Friday 10th February 2017 at Flatford Mill in Suffolk, England. Click here for details and to register.

Monday 24th to Friday 28th July 2017 at Edinburgh Genomics in Edinburgh, Scotland. Click here for details and to register.

 

 

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