The game HelloDNA came about during the first St. Petersburg Hackathon on bioinformatics BioHack, which was held at ITMO University.
How and when did the idea for this application that can explain some of the basic concepts of bioinformatics, come about?
Yulia Kondratenko: At the Hackathon, you could take any task that was offered, but we decided to come up with our own. We discussed a few ideas, met several times before the hackathon, and understood that it would be more interesting to do a game. First of all, it required us to become familiar with new technologies, and secondly, we were actually interested in playing the game ourselves.
Our team has two people who know bioinformatics, that is Nastya and I, we are studying in the Institute of Bioinformatics, and we also have an Android-developer Daniil Drukarev, who used to study at ITMO University. We invited him because he has much more experience with writing programs in Java. We had programmed in Python before, but we had only just starting learning Java. During the Hackathon, while working on the project, we learned a lot of new things.
Is your game suitable for everyone or do you need to have some background in bioinformatics?
Anastasiya Gainullina: The game is absolutely for everyone. We made it so that it would be accessible and understandable for any person, not necessarily those who have knowledge or background in biology, computer science or bioinformatics. There are some clues, and as long as the user reads them, he or she can understand what to do. The game is based on Tetris, as its setup is very intuitive.
Yulia Kondratenko: The game simulates the process of alignment of DNA sequences which is something that occurs in real life. At the bottom of the screen, you can see the genome, and from the top, like in the Tetris game, the so-called “reads” fall. The user has to move the “read” to the right or left in order to align it correctly. The better the alignment, the more points the user gets.
A “read” is a fragment of a DNA molecule, which is read from a section of the DNA. There are certain devices which read these fragments but sometimes errors occur. Also, a discrepancy can arise, for example, due to mutations. Thus, for various reasons, this fragment might not fit with the place from which it was read. Bioinformatics specialists can find out from where this fragment was read, and, even if they are not identical genomes, the area from which they were taken. Our game depicts this process, and with time, these small pieces (reads) also start to significantly differ from the areas where they need to be “dropped”.
The game allows the user to control the process of aligning DNA sequences, but how do you explain to those who have no idea, why this process is necessary?
Yulia Kondratenko: From a practical point of view, DNA sequencing is done for diagnosis. For scientists, it’s really important, naturally, and for thousands of other reasons. For instance, it can help diagnose aptitude to certain illnesses, or be used for paternity examination.
The application makes it clear that the genome reads can have mistakes, and these mistakes make the work of scientists more complicated. And yet, the task remains solvable, although once you have a certain number of mistakes you can lose the opportunity to distinguish the proper position of “reads” in a genome.
Anastasiya Gainullina: Also, we wanted to push the user on a path of learning something new, so he becomes interested, and understand where these reads come from. Or why, for example, a genome is large, but a read is so small?