Hamming distance project

Initial problem

• Bottleneck in computation: parallelized python code to calculate hamming distances from large set of gene expressions
• Pre-processing step that takes many hours to complete even using many cores

What we did

• Replace with a highly optimized c++ version
• Packaged as a python library to fit into the existing user workflow
• Set up Continuous Integration to provide automated testing and deployment of the code

Result

• Code now runs in minutes on a single core