Bioinformatics computing in an alternate open-source universe
Thursday, September 12, 2013, 6:00pm
Senior Director, Joyent Inc., Vancouver
formerly, Principal Investigator, Research Center of Excellence in Mechanobiology, National University of Singapore
In 2012 while at the National University of Singapore, I released the TraDES-2 package into open-source. While this package samples large numbers of disordered protein 3D structures, lessons from its development and deployment apply to many other Bioinformatics projects.
I will show how a naive marching-cube solvation algorithm improves the speed and accuracy of protein surface calculations, and how assumptions about hydrophobic core pockets have skewed accessible surface area calculations. I will explain how in-memory pipelines meet the performance needs for making millions of structure samples. I will show how DTrace is used to profile and optimize the performance of the TraDES-2 code. And I will briefly explain how new work I am doing applies to the problem of the re-analysis of large Bioinformatics data sets.
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 4:30-5:30pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC