Software engineer - Python
at Human Genome Sequencing Center, Baylor College of Medicine

The HGSC Clinical Informatics team is looking for a software engineer to architect and implement a system to manage and monitor the analysis tools and data flows that make up the clinical pipelines.


The HGSC provides a unique opportunity to gain high-throughput production experience in an academic research environment, with opportunities for publication, conference travel and international scientific collaboration. As a member of the the NGSI Clinical Informatics team, you will directly contribute to the HGSC’s pioneering work in Mendelian genomics and multiple NIH Precision Medicine initiatives.


The next-generation sequencing informatics (NGSI) team oversees the day-to-day logistics of all NGS pipelines through a single, integrated system that supports the HGSC Sequencing and Analysis Efforts. Within that larger group, the HGSC-CL informatics team focuses on the center’s growing list of clinical projects and partnerships. The many well-defined and funded HGSC projects offer our talented staff the freedom to innovate and the satisfaction of delivering actionable results.


HGSC-CL Software Engineer Duties:



  • Clinical Production Informatics

  • Design and implement a software system that routes several separate data sources to the appropriate analysis pipelines and delivers data to upstream systems.

  • Support and Troubleshooting

  • Interact with PMs, Clinical Geneticists, LIMS, and IT

  • Provide feedback to NGSI Production R&D

  • Build and maintain monitoring tools

  • Performs other job-related duties as assigned.


Skills & Requirements


Education and Experience:



  • Minimum Education Required: Bachelor's degree in Computer Science or related field.

  • Minimum Job Experience Required: Two years’ experience in software engineering.

  • Preferred: At least 1 year of at-scale NGS experience.

  • Experience in the following:

  • Unix command line interface

  • Programming Language (python preferred; ruby, java, perl, C++)

  • Familiarity with databases and sql.

  • Git


 The ideal candidate will also have the experience with some of the following:



  • Software Engineering methodologies

  • CAP/CLIA Documentation

  • High Performance Compute Environment (e.g., moab)

  • Web frameworks

  • Software testing

  • Cloud computing / AWS / DNAnexus