Programmer Analyst II

Department: 
HGSC:INFORMATICS-NEX GEN
Location: 
Texas Medical Center, Houston, TX
Description: 

The Human Genome Sequencing Center (HGSC) at Baylor College of Medicine was founded in 1996 under the leadership of Dr. Richard Gibbs and is a world leader in genomics. The the primary mission of the HGSC is actionable translational research across the full spectrum of human health and disease using large-scale genomic data to drive collaborative analytics, gene-phenotype discovery and clinical innovation. As a Center for Common Disease Genomics funded by the National Institutes of Health, the HGSC provides a unique opportunity to work on the cutting-edge of genomic science at the center of Houston’s Texas Medical Center. With approximately 200 employees and occupying 36,000 square feet of BCM’s Alkek Building, the HGSC boasts state-of-the-art sequencing and High Performance Computing technology. Resources include a cluster with more than 3 million CPU hours per month sitting atop 8 PB of live disk, which serves as the foundation for high-throughput production, research analytics, software development, an expansive integration with AWS cloud-computing resources, and a local Hadoop distributed compute infrastructure. Over the next five years the HGSC will sequence more than 100,000 samples and manage close to 100 PB of data for both our research efforts and our newly established clinical lab, the HGSC-Clinical Laboratory.

 

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.

 

  • Clinical Production Informatics:
    • Designs and implements software system that routes several separate data sources to the appropriate pipelines.
    • Supports and Troubleshoots
    • Interacts with PMs, Clinical Geneticists, LIMS, and IT
    • Provides feedback to NGSI Production R&D
    • Builds and maintains monitoring tools

Required:

  • Bachelor's degree in Computer Science or related field.
  • Two years’ experience in software engineering.

 

Preferred:  

  • At least 1 year of at-scale NGS experience.
  • Unix command line interface
  • Programming Language (python preferred; ruby, java, perl, C++)
  • Familiarity with databases and sql.
  • Git
  • Software Engineering
  • CAP/CLIA Documentation
  • High Performance Compute Environment (e.g., moab)
  • Web framework
  • Software testing