Senior LIMS Software Engineer

Personalis, Inc. is a leader in advanced cancer genomics for enabling the next generation of precision cancer therapies and diagnostics. The Personalis NeXT Platform® is designed to adapt to the complex and evolving understanding of cancer, providing its biopharmaceutical customers and clinicians with information on all of the approximately 20,000 human genes, together with the immune system, from a single tissue sample. In population sequencing, Personalis operates one of the largest sequencing operations globally and is currently the sole sequencing provider to Veterans Affairs' Million Veteran Program. To enable cancer and population sequencing, Personalis' Clinical Laboratory was built with a focus on clinical accuracy, quality, big data, scale and efficiency. The laboratory is GxP-aligned as well as Clinical Laboratory Improvement Amendments of 1988-certified and College of American Pathologists-accredited.

Located in Menlo Park, CA, Personalis’ genome analysis and interpretation services will help clinical researchers and physicians use genome sequence data to help elucidate underlying disease mechanisms, improve the diagnosis of genetic disorders, guide treatment and drug choice, and anticipate and prevent diseases.  We are seeking a talented and highly motivated, Senior Laboratory Information Management System (LIMS) Software Engineer to join our Team.

Summary:

As part of the overall LIMS & Data Management group, you will be a key member of a team of engineers and analysts, focused on the development and support of lab information systems.  The main goals will be to develop a highly automated lab and achieve a substantially shorter sample turnaround time.  The position reports to the LIMS Auxiliary Manager.

RESPONSIBILITIES:

• Work closely with a variety of internal stakeholders to:
• Design, development, and deploy improvements and extensions to the LIMS, as well as associated lab instruments and software systems.
• Implement mechanisms for tracking key process, performance, and business metrics.
• Provide maintenance and support for day-to-day lab operations, including the troubleshooting of lab instruments, barcode printers, lab scientists’ workstations, etc.
• Proactively identify areas for process improvements, and generate software solutions for them.
• Perform IQ, OQ, and PQ on the LIMS and related systems, and prepare the associated documentation.

REQUIRED EDUCATION/EXPERIENCE:

• M.S. in Bioinformatics, Computer Science, Biology, Physics, or a related field, plus 5 years of work experience; or an equivalent combination of education and experience.
• Proficient full-stack developer with strong database design and development experience, preferably in MySQL and PostgreSQL.
• Fluent in Python, Java a plus.
• Working experience with Python web framework such as Flask or Django, as well as Jinja2 templating language.
• Good knowledge of front-end technology such as HTML5, CSS, JavaScript.
• Good knowledge of SQLAlchemy ORM.
• Experience working in a Linux/UNIX environment.
• Experience supporting high throughput lab information systems in a production environment.
• Experience working with lab scientists on software development and/or analysis projects.
• Basic familiarity with NGS data sets and analysis tools, with a preference for the Illumina platform.
• Detail-oriented work style.
• Collaborative approach to identifying problems and implementing solutions.
• Excellent communication skills.

DESIRED EXPERIENCE:

• Experience with developing and supporting software in a regulated environment, e.g., CLIA, CAP, etc.
• Experience with the LabVantage software system.
• Experience with HPC environments.
• Familiarity with industry software development procedures, in particular Agile development strategies.
• Knowledge of basic statistics.
• Experience in data visualization.

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