We are committed to sharing the resources we generate freely. Most of these are publications and software, but other types are listed here.

Databases

PopPUNK databases

A list of pre-built databases for PopPUNK can be found at https://www.bacpop.org/poppunk/.

Training and teaching

Intermediate programming course

This course which is aimed at helping improve programming skills of bioinformatics/computational biology graduate students and postdocs. The notes are self-contained and are freely available: https://iprogramming.bacpop.org

They currently cover:

• Optimising code
• Running code efficiently on HPC systems
• Compiled languages, data structures and object-oriented code
• Software engineering techniques

From the intro:

This course/book is designed as your ‘second course’ in programming. It is assumed you’ve done a first course which taught you the basics of programming in an interpreted language (probably either python or R), and have now had some experience at using these in your research.

You might have felt that your code is holding you back, and that if you could make it faster or use less memory you could take your analysis further. Or you might have got a solution but are unsure whether it’s the right approach, or whether you could make it better.

Sometimes seeing the impressive (but sometimes intractable!) code and methods we use for research in bioinformatics can feel intimidating, and I feel there isn’t much formal guidance on how to engineer your code this way.

My hope is that this course will give you some extra skills and confidence when developing and improving your research code.