The big light model of DNA rising from the water to close the opening ceremony of the latest Olympics symbolised the great importance of the exposure of the human genome. This milestone wouldn't have been reached without the help of bioinformatics, which is according to many the science of the future. It's the intersection of two disciplines that are getting more and more important: biology and informatics. Developments in modern biology have already named the 21st century as the "Century of the Life Sciences."
And to show the meaning of informatics, I only have to refer to the recent growth in popularity of the World Wide Web and the ever-growing influence of computers on our daily lives. In the Netherlands, bioinformatics was introduced about 5 years ago, and it has since been a booming field of research, already leaving its mark on Dutch life science research. I would like to take you on a tour around the Dutch bioinformatics world, showing its current state and the future opportunities it provides.
What's Bioinformatics About?
Bioinformatics is a relatively new research discipline, with roots in the United States and the United Kingdom. The first bioinformaticians probably appeared in the 1960s, working on computerised molecular graphics. However, the large-scale genome sequencing projects of the 1990s really put bioinformatics into place in countries such as the Netherlands. Nowadays, almost every university city in the Netherlands has its own bioinformatics group or is planning to start one.
Bioinformatics tries to solve biological problems by using computers to make sense of the large amounts of data that arise from sequencing and other large-scale projects. In drug design, for example, the function of a protein is determined by sequence comparison and 3D modelling programs. For another example of bioinformatics, I will tell you a bit about my own research, and then give an overview of how this field is organized in the Netherlands.
The Tim Hulsen Story
I'm currently working as a Ph.D. student on a collaboration project between the Centre for Molecular and Biomolecular Informatics ( CMBI), the bioinformatics department of the University of Nijmegen, and NV Organon, one of the Netherlands' biggest pharmaceuticals. The aim of my research is to use several methods that determine protein orthology (common ancestor) relationships and test which one can be best used for prediction of protein function. Orthologous proteins often perform the same function, but in different species.
For example, if you want to transpose the function of a protein in a model organism to the corresponding human protein, you can make use of orthology to detect the right protein. Most orthology determination methods make use of sequence comparisons: the amino acid sequences of all proteins in two species are compared with each other, and the two sequences that are most similar are considered to be orthologs. I've almost completed this study, so it's time to apply the results in Organon's drug discovery research. This is one of many examples in bioinformatics where fundamental scientific research is combined with applied research.
To become a Ph.D. student in bioinformatics was not always an obvious choice for me. Like many bioinformaticians, I have a background in biology, in which I obtained an M.Sc. degree at the Radboud University Nijmegen in 2001. During my 4-year study, I did two 6-month training periods: one in molecular animal physiology and one at the CMBI. Before I started the latter, I had already made some personal Web sites as a hobby, using several popular scripting languages that would also be useful in bioinformatics. Afterwards, it was obvious that I was more interested in computers than in laboratory work; while working with computers, I didn't have to wait for experiments to run and I could make my own time schedule, independent of the available equipment.
Finally, perhaps because I have two left hands too, I went for a career in bioinformatics. However, I was not sure if I wanted to do a Ph.D., so I sent an "unsolicited application" for a job to Organon, where I was accepted, on a temporary basis, as a bioinformatics researcher. After I worked there for a year on several bioinformatics projects, I decided to do a Ph.D. after all. (Please read my previous article about why I made this decision and about the differences between academia and industry.) With the collaboration the company already had with CMBI, it was clear that I could do my Ph.D. partly at CMBI. I've been working there for almost 2 years, spending some days a week at CMBI and the other days at Organon.
The Netherlands has three major academic bioinformatics departments, of which the CMBI is the biggest. This institute collaborates a great deal with national and international organisations, both private and academic. It also has strong bonds with non-bioinformatics research departments at the University of Nijmegen, helping these departments by solving their arising bioinformatics problems. Other important bioinformatics centres are located at Wageningen University and at the Netherlands Cancer Institute in collaboration with the Academic Medical Centre in Amsterdam. Companies that house the major non-academic bioinformatics departments are Organon, Unilever, and KeyGene.
One thing that is appealing about Dutch bioinformatics is that there are good opportunities to get funding. In 2002, the Dutch government earmarked ?190 million for the foundation and support of the Netherlands Genomics Initiative ( NGI), whose aim has been to put the Netherlands in a leading position in scientific and industrial genomics within the next 5 years. Developing bioinformatics has been one of their top priorities, with a strong focus on collaboration between and among bioinformatics groups.
To achieve this goal, NGI set up the Netherlands BioInformatics Centre ( NBIC) as one of their technology centres. At this foundation, universities, research institutes, and private companies work together toward a central Dutch bioinformatics strategy. NBIC has three main divisions, of which their application service provider BioASP is probably the most interesting. It covers all popular bioinformatics programs and services, as well as giving an overview of news, courses, and projects. BioASP offers a good starting point when looking for a job or funding in bioinformatics. (The other two divisions are BioRange, which fosters co-operation between and among bioinformatics research entities, and BioWise, which co-ordinates education in bioinformatics.)
In a broader perspective (i.e., genomics instead of bioinformatics), NGI provides funding for innovative genomics and bioinformatics research through the "Horizon'" programme. The Horizon Breakthrough Projects--for short-term (1 to 1.5 years) projects with a high-risk profile--are a perfect means to establish "proof of concept'" for wild and crazy ideas. Successful "breakthroughs'" can then be further developed with the Horizon Projects funding. The Horizon Web site provides more information about application deadlines.
A variety of people work in the field of bioinformatics. Bioinformaticians are usually biologists or chemists, but M.D.s and informaticians are also moving into the field. Because of the relatively recent development of bioinformatics, many courses have become available to retrain this wide range of scientists. Molecular biologists and chemists often need to learn some programming or get an explanation of the technical side of bioinformatics programs, but they don't have to worry about not having enough programming skills.
To be a good bioinformatician, it is enough to learn one, easy-to-learn, high-level programming language such as Perl or Python. Timesaving modules are available for these languages that specifically aim at bioinformatics, such as Bioperl and Biopython. It's really not necessary to know all the ins and outs of all kinds of programming languages, since all a bioinformatician does is text parsing and database management. Knowing a great deal about programming could even be a disadvantage, because a professional programmer generally aims at beautiful, well-programmed computer scripts, whereas bioinformatics is all about getting biological relevance from your data. On the other hand, for informaticians some basic biology courses or an introduction to the biological background of bioinformatics tools will prove quite useful.
CMBI provides all necessary courses, of which a course overview is available at their Web site. Most courses are free of charge and open to beginning bioinformaticians. Wageningen University also offers a number of courses, of which most are listed. Of course, taking one of these courses doesn't turn you into a professional bioinformatician, but it gives you a head start in a field that needs people with long-term experience.
For a master's degree, this basic knowledge should be enough. Some institutes even allow you to start a master's without real bioinformatics knowledge, but will require relevant bioinformatics courses during the master's study. If you already have enough bioinformatics experience and want to find a job in the Netherlands, check the Workgroup Bioinformatics or JobReport. Currently, there are still more vacancies than there are people to fill them.
If you are looking for an environment where the male-to-female ratio is about 1-to-1, forget about bioinformatics; apparently men are more attracted to computer work than women. Moreover, the computer-oriented environment creates an atmosphere in which colleagues may have less contact with each other than they would in the lab. Working in molecular biology often means waiting for a gel to run out or a centrifuge to stop spinning, which provides a good opportunity to catch up with colleagues. A computer can be used all the time, which is an advantage but also a disadvantage; a bioinformatician needs to tell himself (or herself in a few cases) to get off the computer and take a break, to talk to colleagues. However, communication through e-mail is obviously much easier than through conversation in the lab. I even know of colleagues who are in the same room but communicate through e-mail. Luckily, there are still coffee breaks for the more social discussions, and of course some things are just better communicated face-to-face than through e-mail; therefore, most groups have weekly meetings to discuss their various projects.
From the overview above, you can see that bioinformatics is a booming field of research in the Netherlands with myriad opportunities. It's becoming a more important field and almost all life scientists and computer scientists are taking part in bioinformatics research. The Netherlands is also an excellent place to do it because of its well-organized infrastructure. Universities and companies are all very close to each other, not only physically but also through tight collaborations. And an organisation like NBIC helps ensure that these institutes are somehow connected with each other. So have a look at one of the Web sites mentioned, and maybe I will see you soon as a bioinformatics expert, somewhere in the Netherlands.