By Matthew Dublin
At the National Center for Supercomputing Applications' Private Sector Program Annual Meeting, the NCSA's Victor Jongeneel presented a talk on HPC bottlenecks and potential solutions that are holding personal genomics back.
According to Jongeneel, one of the biggest challenges is the lack of scalability for popular genome alignment and assembler codes. For example, his team ran a test on ABySS, assembling a modest sized genome of a yeast and found that, based on wall clock and memory requirements, the code is inherently not scalable. Ultimately, Jongeneel says that this is a result of the fact that many folks developing genomics software are not professional developers, and while the code is complex and innovative, most bioinformatics code is not up to the standards of the HPC community.
When an audience member who identified himself as a representative from Microsoft asked Jongeneel about what the ideal solution might be to this problem, he responded that since most of the code that is produced is research grade, and the technology moves so quickly, it often renders "new" code obsolete in a short time. He went on to say that commercial attempts have also fallen short of addressing these challenges for the same reason, because as soon as scalable solution is produced, the rapid movement towards a new solution leaves them in the dust. Jongeneel said that ultimately a fundamental rethinking of compute architectures that allow for workflows with multiple complex steps will be key for making personal genomics a reality.
Click here to watch the whole presentation.
