Bioinformatics and Genomics – Professional Development Day

The 4273π project, SSERC and Edinburgh Genomics will deliver a professional development day for those involved in teaching biology at schools. The focus will be on current bioinformatics and genomics, practical activities suitable for pupils, and links to Curriculum for Excellence Higher Biology and Human Biology.

The event will be held at Edinburgh University on 23rd August 2016. Early booking is recommended.

Further details are available from SSERC.

Free loan boxes for schools

We provide free loan boxes to schools who are interested in teaching and learning bioinformatics. Each loan box consists of 10 Raspberry Pi computers and all necessary peripherals, apart from monitors. The loan boxes come installed with the latest version of our 4273π materials, suitable for sixth-form level and with links to the Scottish Higher curriculum in Biology and Human Biology.

Raspberry Pi computer. Images © Heleen Plaisier.

The loan boxes were made possible thanks to funding from Teachers Together and Access for Rural Communities projects at the University of St Andrews. This allowed us to buy lots of Raspberry Pi Model 2 computers, Rii keyboards, USB power adaptors, powered USB hubs, VGA to HDMI adaptors, extension cords and micro sd cards.

Unpacking lots of Pi computers and paraphernalia. Images © Heleen Plaisier.

The loan boxes were first used during the Teachers Together Conference in 2015 at the University of St Andrews. Teachers Together is a partnership that encourages links between Higher Education and schools. Around 50 teachers from Scottish State Schools attended the conference, and they were given the opportunity to learn more about selected disciplines within the University.

Teachers Together 2015. Images © Fraser Cameron.

A group of around 20 teachers chose to be introducted to the School of Biology at the University of St Andrews. The group first attended an introductory talk by Dr Jacqueline Nairn, and afterwards learnt about PCR techniques and bioinformatics. The 4273π team gave a hands-on demonstration of the Raspberry Pi and some of the 4273π materials for learning and teaching bioinformatics.

As you can see on Fraser Cameron’s photos below, the teachers “really enjoyed learning something new”. They said the best part of the worshop was the “introduction to Raspberry Pi”, and “getting to experiment on the computers, something I don’t get the chance to do much”, and that they were “previously unaware of the technology”. They appreciated the “practical help and explanations”, and thanked the team “for helping me and explaining without making me feel clueless”.

Teachers Together 2015. Images © Fraser Cameron.

Our loan boxes are provided free of charge and are intended for short- or medium-term use. Loan boxes are available to any state school in Scotland. Schools participating in Access for Rural Communities or Teachers Together will receive priority. Currently, 4273π loan boxes are not available for independent schools or schools outside Scotland.

When we deliver the loan box, we would like to demonstrate its use to teachers and/or pupils. We are happy to co-lead activities with the loan box, either to whole classes or voluntary groups of pupils at your school. To register your interest in borrowing a loan box, please email 4273_pi@ed.ac.uk with “LoanBox” as the subject. In your email please include:

  • Your name and daytime telephone number
  • School name and local authority (must be in Scotland)
  • Ideal date and duration of loan
  • Alternative dates/durations
  • Whether you require 4273π project members to co-lead an activity for pupils

Due to high demand, we may not be able to match your request precisely. Please indicate as much flexibility as possible.

Loan boxes, assistance, demonstrations and activities are provided free of charge. For funding 4273π loan boxes, we are grateful to the Access for Rural Communities project and the Admissions Department at the University of St Andrews. Loan box delivery, demonstration and activities are also supported by the University of Edinburgh.

Version 1.4 released

We are delighted to announce the release of version 1.4 of 4273π on March 10, 2016.

Version 1.4 can be downloaded here:

  • 4273pi.tar.gz (SD-card image and documentation; 7 GB as-is, 30 GB uncompressed, SHA-11919d42a62dfcaf321d0cfcc456b8846f0aafa46)

This version includes updated materials and operating system. It should run on any model of Raspberry Pi.

As an experimental new feature, version 1.4 of 4273π  includes the Bioconductor package for analysis of high-throughput genomic data. For example, start R then try:

library(Biobase)
library(limma)
library(hgu133a.db)

 

Welcome to Dr Heleen Plaisier

The 4273π project is delighted to welcome its first dedicated employee, Dr Heleen Plaisier!

Heleen has been part of the project since the start, and was part of our first-ever school event in 2014. Heleen also brings major experience in science outreach, teaching, editing, project management, research and botany.

As of 1st February 2016, Heleen is a Postdoctoral Research Associate in Bioinformatics Education at the University of Edinburgh, working on all aspects of 4273π. Heleen is based in the Institute of Evolutionary Biology which is the new centre for the project – Dr Daniel Barker also moved here in January.

We look forward to working with our friends and colleagues across the UK and around the world, expanding the project with new vigour!

Feel free to contact Heleen at: 4273_pi@ed.ac.uk

New papers using 4273π

Three papers using 4273π have been published this month! All open access:

Robson J.F. and Barker D. (2015) Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer. BMC Research Notes, 8, 561.

Wregglesworth K.M. and Barker D. (2015) A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1. BMC Research Notes, 8, 565.

Barker D., Alderson R.G., McDonagh J.L., Plaisier H., Comrie M.M., Duncan L., Muirhead G.T.P. and Sweeny S.D. (2015) University-level practical activities in bioinformatics benefit voluntary groups of pupils in the last 2 years of school. International Journal of STEM Education, 2, 17.

Welcome to 4273pi.org

Welcome to the new online home of the 4273π project – bringing you free bioinformatics teaching material, and events for schools and the public!

Since 4273π is now well over two years old, it seemed we should have our own domain. Here it is! http://4273pi.org

Please look out for improvement and expansion of the 4273π Web site over the coming weeks.

You can also find us on Twitter, Facebook and Linkedin.