Page Content: She is crazy about her work and never has enough time to do all that can be done. The job also comes with some serious hardware – like a high performance computing cluster boasting over one Terabytes of RAM, more than 200 processors and over 60 Terabytes of storage.
Meet Anelda van der Walt, a bioinformatics analyst in the DNA sequencing unit at Stellenbosch University's Central Analytical Facility.
What is a bioinformatician?
Bioinformaticians are scientists who work on some aspect of Life Sciences research with their main research tools being computers – they analyse data, develop software, or develop algorithms to deal with complex problems, such as finding cures for dangerous diseases. Bioinformaticians can work in a laboratory and perform their own experiments and generate their own data or they can use data generated by other laboratory specialists to work on.
How does one become a bioinformatician?
The reality is that you can come to Bioinformatics from basically any field. One of my colleagues studied Actuarial Sciences, another Applied Mathematics, and another Microbiology. Even medical doctors and engineers can move into the field of Bioinformatics. As far as I know there are no undergraduate degrees in Bioinformatics in South Africa at the moment, but there are several institutes offering postgraduate courses such as Honours, Masters, and PhDs in Bioinformatics. There are also minor introductions to Bioinformatics at some universities as part of various undergraduate subjects such as genetics, biochemistry, and microbiology.
My career started with a BSc degree at the University of Pretoria, and then Honours at Stellenbosch University with Genetics as my major subject. I then completed an MSc in Bioinformatics at the South African National Bioinformatics Institute at the University of the Western Cape.
Describe a typical day in the life of a bioinformatician?
Sitting behind my computer! There are various "flavours" of bioinformaticians. If I can use the study of proteins as an example: you might be looking at three dimensional (3D) modelling of protein structures to find biological functions for the protein of interest. If you are more mathematically inclined, you can develop new algorithms to improve the way 3D modelling is done, or you could be writing software that can be used by biologists to perform 3D modelling of your protein molecule. Some bioinformaticians might be more closely associated with the biology and you may prepare your own samples in the laboratory and perform your own data analysis and even do some minor scripting (writing little programs). It really can be whatever you want it to be, with as much or as little programming as you like.
Why do you think this kind of work is important?
Over the past few years technological advances in the genomics field have led to huge increases in the data volume that can be produced in laboratories. Biologists and medical scientists cannot find important clues in these huge datasets via traditional analysis methods. Bioinformaticians support biological and medical research by finding ways to move, store, analyse, and interpret these large datasets. Without Bioinformatics the human genome would not have been sequenced and Angelina Jolie would not have known that she is at risk of developing cancer later in life.
What kind of research can be done using Bioinformatics?
If you are in a Life Sciences related field and you are generating data and analysing it on a computer, you are using tools and algorithms developed by bioinformaticians (excluding of course Microsoft Excel). Some of the projects currently running in South Africa that are making use of bioinformatics, include human genome sequencing to look at genetic causes of various genetic diseases and cancers; genomics analysis of interesting animals such as sharks; biodiversity studies; food scarcity related projects; and development of software for data analysis. But these are only the tip of the iceberg!
How do you stay up-to-date with what is happening in this field?
I read articles published in academic journals, follow blogs of experts and attend national and international conferences. Did I mention read, read, and more reading?
What do you like the most about your work?
I love most aspects of my job. But what I like the most is the opportunity to be part of a very diverse group of scientists that gets to work on unbelievably interesting and challenging projects. I also enjoy working with people who are very passionate about their research. There are three things I absolutely cannot do without: my Mac, my high performance clusters, and some great colleagues.
What do you dislike the most about your work?
The fact that I do not have enough time to do everything there is to do.
Where do you see this field going in the future?
There are no limits. The "big data" problem has only recently arrived in the Biological Sciences domain. There are uncountable unsolved problems related to health, populations, conservation, and food scarcity, to name but a few. Bioinformatics is definitely here to stay.
Would you recommend this career path?
Yes absolutely. If you enjoy problem solving and interesting challenges, bioinformatics is a phenomenal field to get involved in. There are several career paths open to you – you can stay in academia, work for industry or even start your own consulting or software development company.
Some cool links to explore:
https://apps.facebook.com/fraxinusgame/
http://circos.ca/intro/published_images/
http://jmol.sourceforge.net/screenshots/
http://human.brain-map.org/static/brainexplorer
Pictured above, an image from the journal Cell, showing a vast gene regulatory network in mammalian cells that could explain genetic variability in cancer and other diseases. Source: http://www.bioquicknews.com/node/600
For more information about the Central Analytical Facilities at Stellenbosch University, visit http://academic.sun.ac.za/saf/about.html
Anelda van der Walt will also feature in the October 2013 issue of Quest magazine.