Graduate Student Researcher
Stanford, Ca, Us
Biologists are trying to answer big questions about life. How closely are we related to other species? What traits are conserved through the evolutionary tree? What implications do these have on diseases and cures for humans?Many clues to the answers are hidden in the over 3 billion base pairs of the human genome. To even know where to start looking, large amounts of computation need to be done on these genomes to extract any understandable information. Because of the sheer length of genomes, these computations quickly become intractable using standard computers. Specialized supercomputers, such as application-specific hardware accelerators, can be used to greatly speed up the processing. However, these are generally highly tuned implementations that don't allow for a biologist to easily play around to experiment with the data.I worked on a specialized hardware architecture and platform for gene sequence alignment that combines ultra high performance with flexibility of programming for biologists. First, I built a desktop-sized, FPGA-based hardware accelerator that is 1000 times faster than a standard computer. Then, I invented a new programming language and compiler framework to easily create new implementations without requiring FPGA design experience. Finally, I developed a software platform that abstracts away the FPGA interface, getting right to the data and results.With this system, the biologist can truly focus on exploring the genome to answer life's biggest questions.