Senior Engineer, Primary Analysis

Pacific Biosciences
Job Location: 
Menlo Park, CA
Job Description: 

Pacific Biosciences develops and commercializes single-molecule real-time DNA sequencing instruments. We are seeking a skilled hardware/software engineer to participate in the development and integration of the signal processing pipeline, which includes the analysis steps of trace processing, pulse detection and classification, base calling, and quality assessment. This senior engineer will (i) develop solutions for enhanced on-instrument parallel processing workflows and data throughput optimization using FPGA hardware acceleration technologies combined with conventional computing ; (ii) develop tools for large dataset analysis and functional/performance regression tests; and (iii) design, develop and test component-level algorithm and implementation enhancements to meet mission-critical accuracy and throughput requirements. This position requires an individual with a strong mix of FPGA hardware logic design, analytical, algorithmic and software engineering skills, who is accustomed to developing product-quality hardware/software according to company coding and process standards.

• Work in a multi-disciplinary organization of software and hardware engineers, bioinformaticians, chemists, and molecular biologists developing state-of-the-art, single-molecule, genomic analysis systems.
• Quickly identify solutions to complex data processing and automation problems for use in production instrument hardware/software and internal tools; provide methods or prototypes for concept evaluation.
• Design, develop, integrate and test analysis pipeline components for deployment in production FPGA hardware and software; develop optimized implementations to maximize performance and throughput on available hardware.
• Write functional specifications and design documentation for peer review; maintain hardware/software development practices adhering to company standards for coding and unit/functional test coverage.
• Provide assistance to testers and support personnel as required to troubleshoot system issues or assist in system-level integration.
• Work with outside vendor to develop optimal FPGA based solution utilizing commercially off the shelf high performance and reconfigurable computing boards.


• M.S. in physical science discipline, electrical engineering, or computer science; candidates with a similar B.S. degree and a high level of relevant experience will also be considered.
• 4+ years of professional experience in algorithm development involving high-performance signal processing, system modeling, and/or machine learning for analytical instruments or systems.
• 4+ years of experience with FPGA hardware acceleration (Verilog/VHDL, SystemC), real-time software, and distributed computing are required.
• 4+ years of professional software development experience (may be concurrent) using C++ in a structured engineering environment. Experience with object-oriented design is required.
• Proficiency with Linux, Windows, and professional software development tools, including IDEs and revision control, is required.
• Experience with multithreaded programming is required.
• Experience in the life-sciences tools domain, especially DNA sequencing, is desired.
• Preference is shown to candidates with strong analytical and development skills who demonstrate the capability to bring solutions beyond the prototype stage for deployment in performance-critical production hardware/software.

About Our Organization: 

Pacific Biosciences’ mission is to transform the way humankind acquires, processes and interprets data from living systems through the design, development and commercialization of innovative tools for biological research. The company has developed a novel approach to studying the synthesis and regulation of DNA, RNA and protein. Combining recent advances in nanofabrication, biochemistry, molecular biology, surface chemistry and optics, Pacific Biosciences has created a powerful technology platform called single molecule, real-time, or SMRT™, technology. SMRT technology enables real-time analysis of biomolecules with single molecule resolution, which has the potential to transform the understanding of biological systems by providing a window into these systems that has not previously been open for scientific study.