Bioinformatics for all: scientific outreach at the European Bioinformatics Institute
Catherine BROOKSBANK
EMBL-European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
Abstract. The advent of genome sequencing heralded a new era for the biological sciences. Previously we spent most of our time in the lab generating data, whereas now we are now awash with data and our efforts must go into finding more efficient ways of analysing it. A new field, termed bioinformatics, evolved to meet this need. The European Bioinformatics Institute is an important hub of research, service provision and training in bioinformatics. As such, we take very seriously the need both to inform the general public and educate the biologists and bioinformaticians of the future about how bioinformatics and the new biology will affect all our lives. Here I discuss some of the outreach activities that we’ve been involved in in the past two years.
Introduction
Scientists have invested a huge amount of time and money into deciphering our full genetic sequence and those of many other organisms. Why? DNA holds the key to how every organism on the planet functions. If we know the sequence of all our genes, we can predict the sequence of all our proteins. We can begin to work out how tiny changes in the sequence of a gene can have profound effects on the function of the protein that it encodes. And by understanding the nature of these changes we can attempt to find rational ways of preventing and treating the diseases that these changes cause. Similarly, understanding the genomes of other organisms is finding application in agriculture, food manufacture, and environmental science. It is therefore vitally important that students, irrespective of whether they intend to pursue a career in science, leave school understanding how this new biology will affect all aspects of their lives – from the diagnosis and treatment of disease to their food supply.
Our responsibility is an educational opportunity
The European Bioinformatics Institute (EBI, www.ebi.ac.uk), which is a part of the European Molecular Biology Laboratory (EMBL, www.embl.org), fulfils a vital public service by making a treasure-trove of biologically important information publicly accessible. This information comes from genome-sequencing projects and other high-throughput projects for gathering molecular biological information (for example protein structures, protein–protein interactions). We do this because we firmly believe that freely available information will accelerate the advancement of science.
The main users of our data resources are, of course, biological scientists. Bioinformatics is a word that few school students or members of the general public have encountered; should we be spending time trying to preach such a specialized subject to them? I would argue that the EBI’s policy of making biological information freely available also provides a wonderful educational opportunity.
In the past two years we have been involved in a number of projects that have brought the the fields of genomics and bioinformatics to pupils, teachers and the general public. The reaction from our participants has been extremely positive: they are often surprised and delighted that they can explore the same data that scientists use on a daily basis to advance our understanding of biology. Here I outline three different events that the EBI has been involved in, and try to draw some general conclusions about how to organize successful outreach events.
1. Exploring your genome: a treasurehunt on the Internet
In summer 2003, EMBL celebrated 25 years in Heidelberg – the home of its central laboratory. As part of the celebrations, it threw open its doors to the populace of Heidelberg. Activities included hands-on practical classes, tours and a science café in which participants could browse exhibits about the laboratory. The EBI organized ‘Exploring your genome: a treasure hunt on the Internet’, as a way of introducing people to the human genome, why it’s been sequenced, what we can learn from the sequence and how genomic information can be linked to other types of biological information to help us learn more about ourselves – in health and disease. The entire activity lasted about 80 minutes; it was held in German and repeated four times throughout the day.
The activity began with a 20-minute introductory presentation that explained what bioinformatics is, the basic biology needed to do the treasure hunt (a primer on the central dogma – DNA makes RNA makes protein), and an explanation of how the treasure hunt would work.
The treasure hunt itself focused on finding out about a mystery gene. Participants (grouped in pairs with one computer per pair) were given a short DNA sequence and asked to find the three bases that code for the start of a gene (the start codon). They then had to translate a short stretch of the genetic code into the protein code (they were given a ‘codon wheel’ to allow them to do this); next they were shown how to do a homology search to find the protein whose sequence they’d translated. They then used several EBI-based databases to find out which chromosome the mystery gene was on, what disease results if there are mutations in the gene, and some structural features of its protein product. Each participant was given a printed workbook in which to write the answers. All the information needed to do the practical was printed in the workbook, and the only other equipment needed was a computer with an Internet connection. Prizes were awarded to all participants, but the team that finished first got an extra prize.
The aim of our activity was more fundamental than to give the participants a taste of bioinformatics and its uses. We tried to use bioinformatics as a vehicle to illustrate some important biological principles, such as the elegant simplicity of the genetic code, the link between genetic variation and human individuality, and the relationship between linear sequence and three dimensional structure. This might sound ambitious but our participants found the concepts involved reasonably straightforward, and they all finished the activity in time. They were surprised that they could access the human genome without restriction and pleased that they’d be able to explore it further by themselves. Some participants expressed disappointment that the practical didn’t involve an activity in an experimental lab, but some of them went on to do another practical as part of their tour of EMBL. The treasure hunt has since been used elsewhere: we successfully adapted it for inclusion in our CEEBT teachers’ workshop (see part 3 below), and one of our volunteers is now using the treasure hunt to teach basic bioinformatics skills to non-biologists at the British Antarctic Survey.
Copies of the workbook can be downloaded from:
www.ebi.ac.uk/~schlitt/Schatzsuche/ (German version) or www.ebi.ac.uk/~cath/treasurehunt.pdf (English version)
2.Wellcome Trust Genome Campus DNA day
This open day (actually two days), held in July 2003, celebrated the completion of the human genome sequence, the 50th anniversary of Watson and Crick’s discovery of the structure of the double helix, and 10 years of the Sanger Institute. The bulk of the organization was done by the Sanger Institute, but with contributions from the other two institutes that it shares the campus with – the EBI and the Human Genome Mapping Project Resource Centre (HGMP-RC). We opened our doors to people from the local villages, secondary schools and primary schools throughout the UK, staff and their families, as well as holding a reception for eminent scientists and representatives from funding bodies.
The centerpiece of the open day was an exhibition in a large marquee in the grounds. Visitors could take themed routes through 19 different displays, exploring topics such as modeling the double helix, codes and computers, the origin of life, databanks, individuality, and ethics. There were different activities and competitions at each stand, all designed to engage the participants rather than just having them absorb information.
Practical activities ranged from a simple ethanol precipitation of DNA (done in a few moments at one of the stands) to molecular diagnostics and histopathology workbenches that took about an hour. There were also regular tours of the Sanger Institute’s Sequencing Centre.
Over the two days we had more than a thousand visitors of all ages, which included school parties from all over the UK. The open day was a resounding success and the Sanger Institute plans to use it as the basis for a permanent exhibition on campus. More information about DNA day is available at www.sanger.ac.uk/Info/openday/.
3. What’s all the fuss about genomes?
‘What’s all the Fuss about Genomes?’, organized by the three institutes on the Wellcome Trust Genome Campus, was one of a series of nine workshops held throughout Europe during 2003 and 2004 as part of a project known as CEEBT – Continuing Education for European Biology Teachers (see www.ceebt.embo.org/ for more information). CEEBT is coordinated by the European Molecular Biology Organization (www.embo.org) and its sister organization, the European Molecular Biology Laboratory (www.embl.org), and funded by the Commission of the European Union under its 5th Framework Programme. CEEBT teachers’ workshops are aimed primarily at secondary school teachers, and especially those teaching 16–18-year-olds. These workshops bring teachers and scientists together for two intensive days of practical classes, lectures and discussions. In so doing, they provide a forum for the exchange of best practice, information and experiences.
Before planning the workshop in detail, we held a brainstorming session with local teachers. This highlighted the need to make as much of the workshop as possible directly transferable to the classroom. Genomics and molecular biology form a small but important part of the biology syllabus for 16-18-year-olds in many European countries; our research revealed that, with the best will in the world, teachers do not have much time in which to teach these topics; preparation time and funds to buy kits and equipment are at a premium. We therefore set out to focus the majority of the weekend on practical exercises that can be done in the classroom with relatively inexpensive materials.
Programme
We had a complex and ambitious programme; space constraints dictated that we ran parallel sessions. After a brief welcome talk and safety briefing, the delegates were split into four groups (labelled A, T, G and C). Each group rotated around two lab-based practicals, a computer-based practical, a DNA modelling practical, two discussion sessions, a tour of the sequencing centre and a small number of keynote talks. There was also an exhibition and the exhibitors gave brief demos during coffee and lunch breaks. The bioinformatics practical was written and run by campus staff; all the other practicals were written and run by staff from the UK’s National Centre for Biotechnology Education, with some help from campus-based volunteers. Each activity had a defined set of objectives that were directly relevant to biology topics taught to 16–18-year olds. For example, one of the practicals provides conclusive evidence that DNA really is the genetic material and shows that DNA encodes protein; the bioinformatics practical (exploring genomes) deliberately used examples of genes and diseases that form part of the UK’s A-level syllabus, and provided an alternative means of teaching these parts of the syllabus.
Participants also had the opportunity to experience for themselves the vast scale of the genome sequencing facilities at the Wellcome Trust Sanger Institute. They familiarized themselves with how genomic data are managed and made available through the EBI’s data resources, and they used some of the tools available to mine and analyse the data. Perhaps most importantly, they had an opportunity to meet some of the scientists who work at the three institutes on campus and to discuss their science with them. These activities complemented the more tightly defined, objective-driven practicals, by providing the delegates with experiences that they would be able to draw on in class.
Lessons learned
We were overwhelmed by the positive responses from the delegates; feedback indicated that the attendees left the campus enthused and raring to transfer this enthusiasm to their students. Over 70% of the delegates completed the feedback form and all said that the workshop either lived up to or exceeded their expectations.
Many of the delegates were delighted (and some were quite emotional) about being able to visit the bosom of genomic sequencing in Europe; they praised the provision of resources that really could be taken straight into class, the clarity of the presentations and the willingness of speakers to answer questions.
One of the greatest difficulties that we faced when organizing the workshop was its effective promotion. However, the process of organizing this workshop has provided us with outlets for publicizing future ones. A more worrying concern is that, although initially we had over 86 registrants, only 56 teachers actually attended. For future workshops we might have to charge a deposit, refundable on attendance, to make sure that we don’t waste valuable places that could have been taken up by enthusiastic teachers.
A full report of the workshop, which includes all the practical protocols and slides from the lectures, is available from www.ceebt.embo.org/countrydescriptions/hinxton.html. Similar reports from the other CEEBT workshops held throughout Europe are available from www.ceebt.embo.org/ceebttw.html.
4. Concluding remarks
What are the ingredients for a successful outreach event? Each event had its positives and negatives (Table 1), but we’ve learned several lessons during the planning of these three events that are relevant to any outreach activity.
Table 1. Pros and cons of each outreach activity
|
Activity |
Pros |
Cons |
| Exploring your genome |
·1 Cheap and simple to run·2 Effective way of teaching both biology and IT skills·3 Participants can do the activity at home or in class if they have access to the Internet |
·1 More effective when coupled with an experimental practical, which drives up the cost·2 Limited to a small number of participants or many repeat runs of the same activity |
| Genome Campus DNA day |
·4 Effective way of reaching many people: overall budget is high but per-capita costs are low·5 Marquee allows participants to explore many aspects of the topic at their own pace·6 Involved the entire campus in the public communication of science |
·3 Needs a large budget (~€75 000)·4 Very time consuming to organize·5 Not practicable for many academic institutes |
| What’s all the fuss about genomes? |
·7 By ‘training the trainers’, has potential to reach many young people·8 Comprehensive·9 Carefully targetted to a specific audience |
·6 Needs a significant budget (~€25 000 for 80–100 participants); per capita costs are high·7 Requires significant investment of time for participants·8 Limited to a small number of participants |
Outreach is a two-way process
Planning any type of outreach event involves educating the scientists who’ll be taking part in the event, as well as educating the participants. The volunteers need to be well briefed about the purpose of the event, its target audience, and what can realistically be done with the time/space/money available. It helps to lay down some ground rules and stick to them (for example, for the Genome Campus DNA day we limited the amount of information that could be put on posters in the exhibition, to make them as readable and clear as possible). If your institute hasn’t run an activity of this nature before, seek advice from educational experts from the very beginning. For example, a couple of hours spent discussing our CEEBT teachers’ workshop with staff at the National Centre for Biotechnology Education (Table 2) made us rethink our plans, and made the entire event much more relevant to our target audience.
Do some market research
This is especially important if you have a tightly defined target audience. For example, to help us organize our teachers’ workshop we had a brainstorming session with potential delegates. This helped us to think about the practicalities (e.g. when to hold the workshop) as well as the science (e.g. how much molecular biology and genomics do 16–18-year olds cover? How can we make the contents of our workshop 100% relevant to their syllabus?).
Do a ‘dry run’ if possible
For example, we tested our genome treasurehunt on the children of some of our staff members to make sure that we’d pitched it correctly and that it wouldn’t take longer than the allocated time.
Keep it simple
You do not necessarily have to go high-tech to generate enthusiasm for your subject. For example, a simple DNA precipitation that took only a few moments was an extremely effective way of bringing practical science to a large number of people at the Genome Campus DNA day.
Add as much realism as possible
The DNA precipitation gave participants a chance to step into the shoes of real scientists. They used the same equipment as a bench biologist would use (Eppendorf tubes, Gilson pipettes) and they performed a task that is an integral part of modern molecular biology. Similarly in our bioinformatics practicals, participants used the same data and tools as biologists use. It’s this authenticity that they find thrilling.
Promoting your activity is VERY important
People won’t come unless they know about it! Plan your promotional campaign right at the beginning and don’t expect more than 5–10% of the people you reach to attend the event.
Seek feedback
It’s difficult, if not impossible, to gauge the long-term success of an outreach event; how do you measure whether your event influenced somone to go into a career in science? But you can at least find out whether your event was stimulating and enjoyable for the participants. If you’re planning to run regular events you’ll need to find out what didn’t work well for the participants, so that you can put it right for next time. Feedback can also be a great motivator for the organizers and volunteers involved in outreach projects. Think carefully about what you need feedback on, incorporate appropriate questions into your evaluation form and, if necessary, provide incentives for participants to return their evaluation forms.
Table 2. A few useful websites
|
URL |
Description |
| www.ebi.ac.uk/2can | 2can Bioinformatics: the EBI’s educational website |
| www.yourgenome.org | A user-friendly guide to genomics |
| Openday websites | An extensive list of educational resources collected for our Campus Openday held in July 2003 |
| www.wellcome.ac.uk/genome | The Wellcome Trust's guide to the human genome |
| www.biology4all.com/ | Useful information for pupils and teachers, including a database of teaching resources |
| www.biology.arizona.edu/ | The University of Arizona's online interactive resource for learning biology |
| www.ncbe.reading.ac.uk | Protocols and equipment for teaching biotechnology in schools, developed at the University of Reading |
| www.ceebt.embo.org/ | This initiative, funded by the European Commission and organized by EMBO, runs workshops and labs for teachers as well as providing online resources |
| www.dnalc.org/ | Educational links, protocols, workshops and more from Cold Spring Harbor Laboratory. |
| www.ase.org.uk | The UK’s professional association for teachers of science |
| www.sciencelearningcentres.org.uk/ | The UK’s national network of centres for the professional development of science teachers and technicians |
Acknowledgements
I am indebted to the following for their support and enthusiasm: EMBL’s Office of Information and Public Affairs, for involving us in EMBL open house 2003; many colleagues at the Sanger Institute, especially Christine Rees, Alison Coffey and David Bentley, for the opportunity to take part in the Genome Campus DNA day; EMBO (especially Andrew Moore and Sandra Bendiscoli) and the European Commission for making the CEEBT workshops possible, as well as my co-organizers, Don Powell (Sanger Institute) and Lisa Mullan (then at the HGMP-RC, now at the EBI); The National Centre for Biotechnology Education, especially Andy Harrison, John Schollar and Dean Madden, for masses of advice and boundless enthusiasm; and my many colleagues at EBI for helping to plan, devise and run the activities discussed. I would especially like to thank Thomas Schlitt, Manuela Pruess, Esther Schmidt, Peter Rice and Rolf Apweiler for devising, translating and running ‘Exploring your genome: a treasure hunt on the Internet’, and a list of people too numerous to mention individually for their involvement in the Genome Campus DNA day. Last, but definitely not least, I thank all the participants in our activities for their enthusiasm and helpful feedback.