Collaborative student research projects published

Two research projects conducted with Middlebury undergraduate students were published in the fall of 2019! The paper “DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark”, describes a distributed reimplementation of the XHMM CNV calling algorithm. DECA began as a Davin Chia’s ‘16.5 Middlebury College Computer Science undergraduate senior thesis project and was further developed by Middlebury CS student Forrest Wallace ‘17 in collaboration with Frank Nothaft at the UC Berkeley AMPLab (and now DataBricks). The paper “MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration” describes a web application for personal genome analysis that can efficiently query whole-genome-scale VCF files. MySeq was designed for educational use and has been used in the CSCI1007 “Practical Analysis of a Personal Genome” winter-term course at Middlebury College. MySeq was developed with Middlebury CS students Leo McElroy ‘18 and Laura Chang ‘20.