Software Engineering

The Software Engineering group’s mission is to solve computational biology problems through software engineering in support of the work of St. Jude Children’s Research Hospital. The group assists the Department of Computational Biology’s discovery efforts by automating commonly used computational workflows and providing hands-on support for computation analysis and data management for large study cohorts. The team also supports method development by providing training and resources tailored to the development of publishable bioinformatics tools. Finally, the group serves the institution through various governance and advisory roles. The Software Engineering Group is tightly integrated with the St. Jude Cloud team.

The Software Engineering group plays both supportive and leading roles within the Department of Computational Biology. Leveraging the high-performance computing facilities in St. Jude’s on-premises data center, the group provides department members with data and pipeline management for large-scale research projects. The group has provided computational analysis for tens of thousands of research samples’ sequencing data, including whole-genome sequencing (WGS), whole-exome sequencing (WES), and RNA-Seq data for projects like the Pediatric Cancer Genome Project (PCGP), the St. Jude LIFE research study (SJLIFE), the Childhood Cancer Survivorship Study (CCSS), and the Pediatric Cancer Dependencies Accelerator (PedDep). 

The group spearheaded the development of St. Jude Universal ID (SJUID), a common, deidentified subject-sample naming system that facilitates data sharing and the coordination of research activities across departments. The group also built and continues to manage the Real-Time Clinical Genomics (RTCG) initiative, a first-of-its-kind protocol for the routine release, via St. Jude Cloud, of appropriately consented clinical genomics data to the research community. 

Software Engineering also builds, maintains, and operates numerous resources on the cloud, including elastic high-performance computing (HPC) environments, databases, and web applications. The team’s experience runs the gamut of programming languages, DevOps technologies, next-generation sequencing (NGS) data types and analysis methods. 

Pipeline Development: Incorporating bioinformatics workflows into our automated pipelines

Research Support: Supporting data and pipeline management for large-scale research projects

Method Development: Training and resources for development of publishable tools

Clinical Support: Custom applications, process development, documentation, validation, and compliance support

Community engagement: Participation in institutional and community initiatives

Michael Rusch

Michael Rusch received a BA in Computer Science from the University of Wisconsin, where he worked for eight years in the Genome Evolution Lab, building software for community annotation of enterobacterial genomes.  He came to St. Jude in 2010 as a software engineer working under Dr. Jinghui Zhang on the Pediatric Cancer Genome Project.  In 2017, he became Director of the Software Engineering Group, where he continues to serve.