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Feature - Amoolya Singh: Computation and biology

Feature - Amoolya Singh, computation and biology


Amoolya Singh in her office at EMBL. All images courtesy of SET-Routes

Editor's note: Readers may recall our series on women in grid computing last March. ISGTW interviewed more enterprising, trailblazing women in science and computing than our month-long series could accommodate! We will continue to bring you these and other personal profiles occasionally.

iSGTW: What do you do?

Amoolya Singh: I'm a computational biologist at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, which is a fancy way of saying I use computers to understand living things.

iSGTW: How did you get interested in this field?

Singh: My interest in science has been mainly shaped by my family origins. I was born and raised in India, in a family of scientists and artists. I remember at the age of five going with my mother to her laboratory and asking what she did. She explained that she took very detailed pictures of the insides of living things. So I asked her if she could take a picture of the inside of me. She promised she would try (although she actually worked on plants and not on humans), and every week I would ask her whether she had done it yet. The art of being a pest (called persistence) was clearly an early trait of mine.

My father was also a biologist. He used to take us on long walks - pointing out trees, flowers, birds and insects, and making up outlandish stories about their secret lives. He often drew on Indian mythology and folklore, but used the Latin names for species. In this way, my early scientific education was entwined with my cultural education. Meanwhile, my mother's brother, a geologist, introduced me to the world of engineering, chemistry and mathematics.

Music has also been an important part of my life. On finishing school, I couldn't decide whether to pursue a career in music or science. After a lot of agonizing, I decided to continue music as a serious hobby on the side, and entered Carnegie Mellon University in Pittsburgh.

iSGTW: What drew you to computer science?

Singh: Originally, I had no intention of studying computer science, since my primary interest was in biology. But the first-year curriculum included a compulsory class in programming. It was a new subject for me, and I was teased by all the guys in the class because I was so clueless about computers. A 45-minute assignment would take me six hours - I was still teaching myself how to type! "Go back to biology," they told me, "this computer stuff is too hard for you." Instead of discouraging me, this only made me more determined to do well. I persevered, finishing the class with an A. I became fascinated that sequences of events could be represented by a programme that was written out beforehand. Around the same time, I was learning genetics and developmental biology (how an embryo grows into an adult organism), and it seemed that there were many conceptual connections between computer science and biology.

The European Molecular Biology Laboratory has research centers located at several universities, including Heidelberg, where Singh works. Image courtesy Heidelberg University.

iSGTW: How did your career progress?

Singh: I then went on to UC Berkeley, where I completed a PhD in computational biology on how bacteria respond to environmental stress and how this process has evolved over millenia. As part of my PhD, I spent a summer at the Pacific Northwest National Laboratory near the Hanford nuclear waste site. Scientists there were studying a uranium-eating bacterium and using computers to analyse its patterns of gene expression. It was very rewarding to put my work to practical use, and I returned to Berkeley at the end of that summer with a renewed sense of purpose and energy. At EMBL, I am continuing to study the evolution of bacterial stress responses, now examining bacteria in the wild ("metagenomes") rather than in the lab.

iSGTW: What's the best part of your job?

Singh: I love science because, like music, it allows me to be creative, to think on my feet, to be playful and retain a sense of childish wonder about the world. By doing science I have also developed as a person: I have learned to accept and respond to criticism, to work with different kinds of people from all over the world, to work hard and have faith in myself, even when it's not clear if a project will succeed, and to take success with humility and failure with humor. All the while, I have remained a dedicated student of music, and have finally stopped wondering if I made the right career choice.

-Dan Drollette, iSGTW. Excerpts from SET-School Ambassadors

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