Coding in the Classroom: Reading the Genome with Raspberry Pi

What is a genome? How do scientists ‘read it’ and how do we use it to learn about our evolutionary history and human disease?
In Code Breaking: Reading the genetic code with Raspberry Pi, London based scientists have developed a teaching module which allows teachers and students to give a go at decoding bits of the human genome by using the Raspberry Pi computer. They write a program in python which allows them to ‘read’ DNA sequence similarly to reading the alphabet three letters at a time. They then use this program to search for cancer mutations, thus highlighting the importance of computation in modern biomedical research.
“The new computing science curriculum wants students to program and create flow charts on real life situations and this project fits in very well. I would have loved to have had students’ actual final code-work annotated and put into their folders as part of the curriculum” said an IT teacher in London’s Maria Fidelis School.
To learn more about the project, follow this link and please feel free to share ideas or your interest in getting involved.


Subject(s)Design & Development, Biology, Computing, Science
Age11-14, 14-16, 16-19
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Dave Gibbs

This fascinating and very topical project is highly relevant to learning in computing including formatting of text output; loops and iterative algorithms and string manipulation. It is the foundation of en excellent collaboration wih science teacher colleagues. 

One key outcome is to get students with an interest in science to appreciate that science is, nowadays, heavily dependent on computer science. It also showcases possible specialist careers paths for computing fans beyond the usual games design and web development paths. 



Olwen Morgan

Hmm .... this might get me some flak ....

I find it understandable but very dispiriting that games programming and web development have been referred to as "usual" career paths. I can recall several conversations in which web developers who called themselves software engineers were told to .... ahem .... consider the benefits of micturating elsewhere ... :-O. Real software engineers know how to develop a system on bare hardware with neither operating system nor program libaries to make life easy for them. The UK suffers chronic shortages of such skills.

I'll acknowledge a web developer as a software engineer when I encounter one who knows how to make JavaScript code provably secure.

Olwen Morgan

For people interested in genome analysis the following titles might be of interest:

Markel, S. and Leon, D., Sequence Analysis in a Nutshell, O'Reilly Media, 2003, ISBN-10:  059600494X, ISBN-13: 978-0596004941

It describes the use of the open-source EMBOSS genome analysis tools.

Currently new copies start at just under £6 from Amazon UK.