Senior Bioinformatics & Genomics Data System Engineer

Natera•San Carlos, CA

1d•$125,800 - $157,200

About The Position

As a member of the Data Science Production Engineering (DSPE) department and DevOps team, the Senior Bioinformatics & Genomics Data System Engineer designs, develops, tests, deploys, maintains, and updates DSPE software tools, data platforms, cloud platforms, automation systems, and analytics systems. The role works with DSPE leadership to produce system architecture and infrastructure design documents, and contributes to reliable and timely delivery of production systems. It also involves monitoring and optimizing performance across metrics such as network and disk I/O, RAM, CPU, and disk-space usage. The engineer contributes to technical documentation and training materials for DSPE Software Engineering & DevOps-owned tools and systems, trains and coaches team members on technologies and best practices, and represents the team in stakeholder meetings. The position calls for bioinformatics and genomics knowledge, Python and AWS expertise, experience with production software and databases, and work in regulated environments.

Requirements

At least a bachelor's degree in Computer Science, Software Engineering, Bioinformatics, or a related field.
Relevant industry experience: at least 6 years with a bachelor's degree, 3 years with a master's degree, or 2 years with a doctorate.
At least 3 years of experience working in a highly regulated environment, such as CLIA- and/or FDA-compliant settings.
At least 3 years of experience working on a Software Engineering or DevOps team.
Demonstrable experience developing and maintaining custom software tools or systems for production environments, preferably high-throughput settings.
Demonstrable experience creating software design specification documents, verification and validation documents, and user manuals.
Excellent understanding of bioinformatics and genomics concepts and NGS technologies.
Excellent Python programming skills and demonstrable experience developing bioinformatics or genomics applications and/or automation systems.
Excellent understanding of AWS services relevant to bioinformatics and genomics applications.
Working experience with AWS services such as Batch, ECS, S3, EC2, and HealthOmics, preferably developing production software tools or systems.
Proficiency with RDBMS systems such as PostgreSQL and/or MySQL, and demonstrable experience developing production database-based applications.
Experience with bioinformatics and genomics file types such as BCL, FASTQ, BAM, and VCF.
Working knowledge of optimizing system architecture and components for performance, scalability, and/or reliability, especially for genomics-scale data.
Working knowledge of system and tool performance evaluation methods and factors such as RAM, disk I/O, and network I/O, particularly for bioinformatics and genomics applications.
Working knowledge of the software development lifecycle (SDLC) and software development and testing methodologies.
Working knowledge of Linux command-line skills and past Linux application development experience.
Proficiency with Git workflows and version control systems such as GitHub and/or GitLab.
Past experience developing automation solutions.

Nice To Haves

An advanced degree.
Experience developing production software tools or systems using AWS services.
Experience developing custom software tools or systems for high-throughput environments, such as those with heavy traffic or high computational loads.

Responsibilities

Ensure timely and efficient delivery of software tools and systems with correct and robust functionality.
Contribute to the design, development, testing, deployment, validation, maintenance, and updating of DSPE software tools and data, cloud, and automation systems.
Work with DSPE leadership to create system architecture and infrastructure design documents that can be efficiently implemented and maintained.
Monitor and optimize software and system performance by evaluating effects on network I/O, disk I/O, RAM, CPU, and disk-space usage.
Create, maintain, and update technical documentation for software tools and systems owned by the DSPE Software Engineering & DevOps team.
Create training materials and contribute to training activities for team-owned software tools and systems.
Train and coach DSPE team members on new technologies, procedures, guidelines, and best practices.
Represent the DSPE Software Engineering & DevOps team in stakeholder meetings.