Last November, a group of biologists, computational scientists, physicists, and chemists held a workshop to discuss the challenges of providing training for end-users of bioinformatics tools.
The group met under the auspices of Serving Life-science Information for the Next Generation, or SLING, a three-year EU funded project aimed at providing tools and training for life science researchers through its five partners: the European Bioinformatics Institute, the Swiss Institute of Bioinformatics, the BRENDA database at the Technische Universität Braunschweig, the European Patent Office, and Enzymeta.
One of the outcomes of the discussion was a paper published last month in Briefings in Bioinformatics that noted that bioinformatics training is challenging "not only because of its interdisciplinary nature but also because of the extensive technological changes witnessed in the field during the last two decades.”
With companies and academic groups releasing tools on a steady basis, researchers have a plethora of resources to analyze their data, but are they utilizing these tools to their full capacity?
BioInform spoke to Maria Victoria Schneider, the training program project leader at EBI and one of the co-authors of the paper, about the challenges facing researchers who want to learn to use these new tools and those who train them. Below is an edited transcript of the interview.
What's the biggest challenge for bioinformatics trainers and trainees?
First of all, it's good to make a distinction. [In the paper] I always refer specifically to training and I make a distinction [from] education. If you look in the literature, there have been some papers and efforts made at the level of education. Whereas in this paper I am concentrating on shorter courses that aim to deliver practical knowledge and skills to a variety of people. It doesn't matter if they are undergraduates or already doing research but these are people that will end up using [bioinformatics] resources.
In the paper, one of the things that we really deal with is training for those that are using bioinformatics resources. We are not talking necessarily of courses where you learn how to program or build databases and so on.
Certainly one of the main challenges is that now bioinformatics is a necessity in biology and in an increasing range of disciplines and it is also a necessity because of the amount of data and the different types of data.
The background of the trainees is another consideration. For example, when you tailor a course for an audience of plant science researchers, you can increase the relevance by making sure the examples are plant based. But when training a diverse group of people, you find out that it's difficult to make everybody happy. This is because trainees work in diverse areas, have diverse backgrounds, and might also have different levels of familiarity with, for example, statistical concepts.
Finally, in many cases, training is not always the priority when applying for grants. This translates into disjointed efforts and lack of long-term sustainability.
You mentioned some specific challenges in the paper but are there any other challenges that aren't mentioned?
The one that we hint at, which I think is very important, is the funding. There is no doubt that if training is always left as the second priority this limits the scope and quality, affecting several aspects, from the training materials to the consistency of support for the trainers.
The ELIXIR [European Life-science Infrastructure for Biological Information] training workpackage report we refer to in the article goes into a lot of detail on things that we suggest should be done. ELIXIR's objective is to create and sustain a world-class infrastructure to manage and integrate information in the life sciences. This is very critical because we are talking about data and resources that are fundamental. These includes databases of primary data that, once lost, would require going back to the lab to collect it all again.
For this particular paper you focus on Europe but do you think there are similar challenges in other parts of the world where these bioinformatics resources are used extensively?
With regards bioinformatics training, my spontaneous reply would be yes. There are very good efforts, especially, for example, in US universities, if we talk about education. They distribute materials [and] they have resources online for the courses so there are things that are happening. But things are still so fragmented. Many times, we are independently doing very similar things so in the end we lose the synergy that we would have if we would work together.
There is a conflict, of course, because people want to train on the resources that either they have been involved with or their institute is involved with. But we should go to a level where we manage to collaborate and share expertise, ideas, and even materials.
Tell me about the three-year grant for the training project.
Well that's the SLING grant, which aims to make sure that advances in European science are supported by the best possible biomolecular information. The training component works to equip researchers to be able to use the databases and services from the project partners. Our training activities under SLING so far have enabled us to deliver training at 10 sites and reach approximately 300 trainees.
Normally, host institutions have funds to cover the traveling costs and logistics for trainers but this is a challenge for many institutions in Europe. The SLING funds enable us to overcome financial hurdles and address the training needs of organizations if they are unable to fund these activities themselves. One of the [requirements of the grant was] that we had to meet with trainers and hosts of these events once a year so that at the end of the three-year grant, we will have guidelines or best practices on how to train and [can] say what we learned through this experience. I did the first of these networking sessions and what came out of that session are all of these ideas that you see in the paper.
One of these is an initiative called the Bioinformatics Training Network. Initially we are developing this with the co-authors of the paper, but we are keen to involve as many bioinformatics trainers as possible because its success will depend on community support and use.
What's the timeline for the BTN to come online?
The BTN website is up and running, however the functionalities will become available in autumn. We welcome expression of interest from those that want to get involved.
In terms of tools that are being developed, is there any effort by the manufacturers of these tools to provide some sort of training?
Well yes. For example, when you create any new software you need to provide some background on how to use it, such as a manual or some documentation. What the ELIXIR training report recommends is that if you provide software or a tool, you should provide a certain minimum amount of supporting materials so that others can train on this.
You touched on this throughout our conversation, but what are some next steps moving forward?
We are thinking of using forums or focus groups. That's key. The main thing is that we start talking. Even if we are training at different levels and different courses, as long as we are talking, sharing experiences, and pragmatically exchanging training materials we can support each other.
For example, there might be people [who] want to incorporate different lectures. It would be nice if we can all contribute to a repository of materials where people can come and find things that are useful. This will also be the best way for us to reach out to people and make our work more practical.
Since the focus so far has been on Europe, will the resources be made available to researchers in other countries?
First of all, the resources and tools at EBI are free and open access. Although the priority of the training has a European focus, our resources are used globally and we do train at an international level. Naturally, our training initiatives are shared with this global audience. We're also in the process of redeveloping our eLearning portal, which will be the natural home for lots of our training materials, open and free to all. And as I mentioned earlier, the BTN will provide a centralized repository for open source training materials.