Evaluating Bioinformatics Teaching across Biosciences Programmes
Professor Iain Sutcliffe and Dr Stephen Cummings, School of Applied Sciences
Project aims
The aims of this project were to survey and define the extent to which the newly emerged discipline of
bioinformatics has impacted upon teaching in bioinformatics in the School of Applied Sciences. Moreover, we
intended to develop staff expertise in this discipline and to conduct research in this area which will be directly
applicable in taught programmes. To achieve this we have:
Carried out an e-mail survey of all academic staff in the School of
Applied Sciences which identified existing and potential users of
bioinformatics techniques.
Built upon existing staff expertise in protein sequence analysis, in
particular for the identification of an important protein family
(bacterial lipoproteins), in order to develop sequence datasets that
can be used in taught modules to critically evaluate online tools.
This has drawn upon ongoing collaborative links with University of
Bradford.
Consolidated expertise in microbial 16S rRNA analysis for the
generation of phylogenetic (evolutionary) trees using the software
programme MEGA4.
Begun a new comparative genomics study exploring the
distribution of proteins from selected cell envelope biosynthetic
pathways that are discontinuously distributed within the bacterial
tree of life. These may ultimately form the basis on new datasets
which can be incorporated into teaching materials.
Developed further collaborative links with University of Ulster on
problem-based learning, who visited UNN in January 2008. Webpages for PBL are currently being developed by the university (see
http://samsara.scic.ulst.ac.uk/~kay/cgi/pbl.cgi) with input from Northumbria staff.
Built external links to researchers at the Centre for Biological Sequence Analysis Denmark Technical
University, a leading provider of bioinformatics tools (http://www.cbs.dtu.dk/index.shtml) which has led
to the receipt of advance proofs of a new textbook (Computing for Comparative Genomics). This text, and
associated online resources run by the DTU, should provide a useful framework for the incorporation of
teaching comparative genomics into taught programmes
Project outputs and dissemination
The outcomes from this project can be categorised into two groupings reflecting the means and extent of their
dissemination i.e. those where the impact is experienced primarily within UNN, and externally relevant
outputs.
Internally relevant outcomes:
The survey of staff expertise and desire to engage with bioinformatics has identified a clear discrepancy
between existing strengths in the staff base and areas that will need to be strengthened to meet the
future challenge of providing a competitive and relevant biological sciences provision. Specifically, we
have a strong staff base for research and teaching utilising bioinformatics as applied to microbiology,
specifically bacterial DNA and protein sequence analyses. This is reflected in the staff base and content of
those modules (mostly located within the biotechnology provision at both undergraduate and Master’s
levels) which are specifically themed around teaching bioinformatics... In contrast, we are clearly weaker
in both research and teaching utilising bioinformatics as applied to mammalian systems, most obviously
and importantly in relation to recent ‘post-genomic’ developments based upon developments from the
human genome project. This conclusion is of particular relevance to future development in the biomedical
sciences provision.
The development of datasets of relevant protein sequences will allow these to be used in bioinformatics
teaching in both specialised bioinformatics modules and in undergraduate and Masters’ level project
work.
Externally relevant outputs:
Publication of a case study article in the Bioscience Education e-journal [Sutcliffe, I.C. and S.P. Cummings
(2007). Making bioinformatics projects a meaningful experience in an undergraduate biotechnology or
biomedical science programme. Bioscience Education e-journal 10, 2. DOI:10.3108/beej.10.2]
Oral presentation and paper in the proceedings of the International Union of Biological Sciences BioEd
2008 symposium on quantitative biology education in Burgundy, France (June 2008; see proceedings at
http://www.ldes.unige.ch/bioEd/2008/bioEd2008.htm)
Critical evaluation of the datasets generated during this project has been incorporated into a review
article for World Journal of Microbiology and Biotechnology [Rahman, O., Cummings, S.P., Harrington, D.J.
and I.C. Sutcliffe (2008). Methods for the bioinformatic identification of bacterial lipoproteins encoded in
the genomes of Gram-positive bacteria. World Journal of Microbiology and Biotechnology, 24: 2377-2382.
http://www.springerlink.com/content/1025494634331241/]
Some of this work was also presented as a poster presentation at a Society of General Microbiology
meeting (Edinburgh, April 2008) [Rahman, O. Cummings, S.P., Harrington, D.J. and I.C. Sutcliffe (2008).
Bioinformatic identification of lipoproteins in Gram-positive bacteria.
http://www.socgenmicrobiol.org.uk/meetings/pdfabstracts/edinburgh2008abs.pdf].
Project impact and evaluation
The project has provided a clear ‘state of the nation’ analysis of the extent to which bioinformatics is taught
within the School of Applied Sciences. There is a clear skills gap emerging regarding programmes administered
from the Biomedical Science subject area and the forthcoming programme review should be considered an
opportunity to rectify this. In this respect, it is important that we are continuing to collaborate with University
of Ulster in the development of relevant problem-based learning units with a view to embedding these in
relevant modules which, in a biomedical sciences context, are most likely to be molecular biology or genetics
modules, rather than stand alone bioinformatics modules. Other online resources have also been identified
(for example: http://www.ls.manchester.ac.uk/research/themes/bioinformatics/resources/;
http://www.ebi.ac.uk/training/handson/; http://www.cs.newcastle.edu.au/~nbi/index.html which may be
useful for either staff development or as the basis of new module content.
Lessons learnt
Microbiology staff contribute most content to the named ‘bioinformatics’ modules and this clearly and directly
reflects their research interests (e.g. molecular phylogeny; protein sequence analyses). Similarly,
bioinformatics content is now embedded within final year undergraduate and master’s level projects
supervised by many staff. However, it will remain a challenge to input new, desirable subject specific skills into
some programme areas, given that this will require both a review of current module content and, perhaps,
staff development activities. The recent expansion in the staff base within the School of Applied Sciences has
brought in new staff with relevant expertise who may be encouraged to participate in this process.