Journal:University-level practical activities in bioinformatics benefit voluntary groups of pupils in the last 2 years of school
| Full article title | University-level practical activities in bioinformatics benefit voluntary groups of pupils in the last 2 years of school |
|---|---|
| Journal | International Journal of STEM Education |
| Author(s) |
Barker, Daniel; Alderson, Rosanna G.; McDonagh, James L.; Plaisier, Heleen; Comrie, Muriel M.; Duncan, Leigh; Muirhead, Gavin T.P.; Sweeney, Stuart D. |
| Author affiliation(s) | University of St. Andrews, University of Manchester, Kilgraston School, Forfar Academy, Portlethen Academy |
| Primary contact | Email: db60@st-andrews.ac.uk |
| Year published | 2015 |
| Volume and issue | 2 |
| Page(s) | 17 |
| DOI | 10.1186/s40594-015-0030-z |
| ISSN | 2196-7822 |
| Distribution license | Creative Commons Attribution 4.0 International |
| Website | http://www.stemeducationjournal.com/content/2/1/17 |
| Download | http://www.stemeducationjournal.com/content/pdf/s40594-015-0030-z.pdf (PDF) |
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Abstract
Background: Bioinformatics — the use of computers in biology — is of major and increasing importance to biological sciences and medicine. We conducted a preliminary investigation of the value of bringing practical, university-level bioinformatics education to the school level. We conducted voluntary activities for pupils at two schools in Scotland (years S5 and S6; pupils aged 15–17). We used material originally developed for an optional final-year undergraduate module and now incorporated into 4273π, a resource for teaching and learning bioinformatics on the low-cost Raspberry Pi computer.
Results: Pupils’ feedback forms suggested our activities were beneficial. During the course of the activity, they provide strong evidence of increase in the following: pupils’ perception of the value of computers within biology; their knowledge of the Linux operating system and the Raspberry Pi; their willingness to use computers rather than phones or tablets; their ability to program a computer and their ability to analyse DNA sequences with a computer. We found no strong evidence of negative effects.
Conclusions: Our preliminary study supports the feasibility of bringing university-level, practical bioinformatics activities to school pupils.
Keywords: Bioinformatics; Computational biology; Secondary school; Raspberry Pi; Open access teaching material; Case study
Findings
Introduction
Progress in Science, Technology, Engineering, Mathematics and Medicine (STEMM) subjects is increasingly dominated by computational analyses. In biological sciences, for example, the exceptional pace of recent advances in technology for DNA and genome sequencing has created a demand for computationally able researchers, to analyse the large amounts of data produced. A field specialising in application of computation to biological problems has emerged, known as bioinformatics. The development of bioinformatics is discussed by Hogeweg[1], and university-level bioinformatics education has been reviewed by Magana et al.[2]
DNA sequences and related data are available at low cost (for new sequencing work) or free in online databases such as GenBank (Benson et al.[3]), Ensembl (Cunningham et al.[4]) and hundreds of others (Galperin et al.[5]). Software for bioinformatics research is usually free, for example the very widely used sequence database search software, BLAST (Altschul et al.[6]). Free resources are also available for bioinformatics teaching and learning, for example 4273π (Barker et al.[7]), Bioinformática na escola (Marques et al.[8]), GOBLET (Corpas et al.[9]), Bioinformatics@school and the EvoEd Digital Library. These publicly available data, software and materials present excellent opportunities for relatively low-cost teaching.
References
- ↑ Hogeweg, P. (2011). "The roots of bioinformatics in theoretical biology". PLOS Computational Biology 7 (3): e1002021. doi:10.1371/journal.pcbi.1002021. PMC PMC3068925. PMID 21483479. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068925.
- ↑ Magana, A.J.; Taleyarkhan, M.; Alvarado, D.R.; Kane, M.; Springer, J.; Clase, K. (2014). "A survey of scholarly literature describing the field of bioinformatics education and bioinformatics educational research". CBE – Life Sciences Education 13 (4): 607–23. doi:10.1187/cbe.13-10-0193. PMC PMC4255348. PMID 25452484. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255348.
- ↑ Benson, D.A.; Clark, K.; Karsch-Mizrachi, I.; Lipman, D.J.; Ostell, J.; Sayers, E.W. (2015). "GenBank". Nucleic Acids Research 43 (Database issue): D30–D35. doi:10.1093/nar/gku1216. PMC PMC4383990. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383990.
- ↑ Cunningham, F.; Amode, M.R.; Barrell, D., et al. (2015). "Ensembl 2015". Nucleic Acids Research 43 (Database issue): D662-D669. doi:10.1093/nar/gku1010.
- ↑ Galperin, M.Y.; Rigden, D.J.; Fernández-Suárez, X.M. (2015). "The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection". Nucleic Acids Research 43 (Database issue): D1-D5. doi:10.1093/nar/gku1241. PMC PMC4383995. PMID 25593347. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383995.
- ↑ Altschul, S.F.; Madden, T.L.; Schäffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. (1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research 25 (17): 3389-3402. doi:10.1093/nar/25.17.3389. PMC PMC146917. PMID 9254694. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146917.
- ↑ Barker, D.; Ferrier, D.E.K.; Holland, P.W.H.; Mitchell, J.B.O.; Plaisier, H.; Ritchie, M.G.; Smart, S.D. (2013). "4273π: Bioinformatics education on low cost ARM hardware". BMC Bioinformatics 14: 243. doi:10.1186/1471-2105-14-243. PMC PMC3751261. PMID 23937194. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3751261.
- ↑ Marques, I.; Almeida, P.; Alves, R.; João Dias, M.; Godinho, A.; Pereira-Leal, J.B. (2014). "Bioinformatics Projects Supporting Life-Sciences Learning in High Schools". PLOS Computational Biology 10 (1): e1003404. doi:10.1371/journal.pcbi.1003404. PMC PMC3900377. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3900377.
- ↑ Corpas, M.; Jimenez, R.C.; Bongcam-Rudloff, E.; et al. (2015). "The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers". Bioinformatics 31 (1): 140–142. doi:10.1093/bioinformatics/btu601. PMC PMC4271145. PMID 25189782. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271145.
Notes
This presentation is faithful to the original, with only a few minor changes to presentation. In several cases citation information was missing and was added to make the reference more useful.
