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4273π: Bioinformatics Education on Low Cost ARM Hardware

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4273π: Bioinformatics Education on Low Cost ARM Hardware

Daniel Barker et al. BMC Bioinformatics.

Abstract

Background: Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access.

Results: We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013.

Conclusions: 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

Figures

Figure 1
Figure 1
4273π screenshot. Practical, Week 7. Predicted gene structures of the Or98b gene in the Drosophila sechellia genome are being compared. Different predictions are made de novo by SNAP [26], run in a terminal on the Raspberry Pi; GeneWise [27], run online at the European Bioinformatics Institute [28], with the D. melanogaster protein being aligned against D. sechellia genomic DNA; and using TBLASTN [1], run online at FlyBase [29]. FlyBase also displays the annotation of this gene from its database. This case study arose during research for a comparative study of the chemoreceptor superfamily in Drosophila[30]. The 4273π background desktop image includes hand-written versions of material from 4273π Bioinformatics for Biologists and from the module BL3320 Practical Statistics for Biologists, which most students at the University of St Andrews would have taken earlier. It also includes a copy of one of the first published phylogenetic trees, from Vestiges of the Natural History of Creation, written in St Andrews [31].

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