Monday, July 28, 2014

PhD tales: (Part 2) Research topic

Deciding on thesis topic for a bioinformatics PhD is one big challenge. There are few PhD students who work on their advisor's funded projects, for whom this is not a challenge. They just work on someone else's idea, what I think. But for others, it is a time to look for their own ideas and interests. Not just ideas but also resources like access to data which is most important in health-related field. Also, it is not just the specific thesis topic but also to decide the broader field of bioinformatics applications, where they want to focus. 

There are various directions where you can streamline your phD studies. One is to focus on your algorithmic and computational skills and try to develop a tool or software that everyone in your community and research can use and benefit from. The other is to go towards the consumer side where you dwell upon the available tools and use it in your favor and come up with new biological findings.
To me it is more useful for the community to help improve upon an existing tool based on your needs rather than reinventing the whole wheel. Having a publication record, as one of the requirements of a PhD is a feature for you to show your potential and caliber. However, software designed for the sake of publication in mind or develop a software with goal of adding just a single feature to outperform or compete among zillions of other tools is injustice towards driving bioinformatics forward. The number of bioinformatics web applications and tools for example sequence aligners, genome assemblers or mappers, and many other bioinformatics software’s are many folds higher than the ones that are actually used.
Also, if I wanted to focus on building algorithm, next thing to do was either look for some other collaborator of our lab for a project that needs a better algorithmic design or find one myself. But for the second direction, I had to only decide on a particular disease that I’m really interested in and practically feasible to conduct research. And for that, Cancer was the very prompt and feasible answer with lots of available online dataset and unanswered questions.
However, there are expectations from not only my advisor but also the department and the peers for a graduate student to only conduct one top-notch research and answer questions never heard before causing cancer. Instead, I desired more to only investigate fundamental questions in biology. I do believe, that from understanding the underlying biological processes leading to cancer oriented changes, new treatments can arise. And I decided to start working working specifically on cancer.

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