Senior infrastructure engineer; [senior] software engineer (high-performance pipelines)

Job Description

Software engineer (high-performance pipelines) – SecureBio The Nucleic Acid Observatory is now SecureBio Detection. Read more SecureBio Projects AI BioTIER Virology Capabilities Test Detection CASPER Zephyr People Our Team Careers Resources Publications MGS Data AI Benchmarks Blog Donate Software engineer (high-performance pipelines) Apply now Project/division: SecureBio Detection Start date: as soon as possible Status: full-time SecureBio employee Approximate compensation: $165,000 to $190,000, depending on experience Visa sponsorship available: not available Work location: in-person in Cambridge, MA strongly preferred The role SecureBio is a nonprofit working to protect the world from catastrophic pandemics. As advances in biotechnology lower the barriers to engineering pathogens, our mission is to ensure humanity’s detection and alert systems are ready. As part of this mission, our Detection team is building a pathogen-agnostic pandemic early warning system: we operate the world’s largest metagenomic biosurveillance network, which performs daily sequencing of wastewater samples and nasal swabs to screen for emerging pathogens. Our computational team develops detection pipelines responsible for rapid processing of deep sequencing data in order to flag potential threats. In pandemic early detection, speed is critical: novel pathogens spread exponentially, so every day of delay means many more people are infected by the time of detection. To meet this challenge, SecureBio Detection plans to more than double our sampling frequency and sequencing volume (currently ~50 billion read pairs per week) while reducing computational end-to-end time from ~12 hours to ~2 hours. As our early warning system scales, we’re looking for a software engineer to help us meet our volume and turnaround time goals. This role will focus on making our metagenomic detection pipelines fast, scalable, robust, and accurate, and will also own pipeline observability. Prior experience with biology or bioinformatics is not required. Responsibilities Pipeline performance: benchmark computational pipelines, identify bottlenecks, and implement optimizations – from CPU cache locality to data flow to complete algorithmic refactors. Pipeline accuracy: improve the sensitivity and specificity of detection algorithms. Pipeline infrastructure: deploy cloud infrastructure, monitor throughput, optimize cost and reliability, maintain databases. Observability and reliability: implement dashboards, expand test coverage, and quickly triage pipeline failures. AI acceleration: stay up to date with rapid AI progress and creatively use AI tools to accelerate your work. (And your colleagues’ work!) Qualifications Must have 2+ years of professional experience in software engineering or a related field Proficiency with performance patterns across the full stack, e.g. memory access patterns, networking, and algorithm asymptotic complexity Creativity in algorithm design Experience with distributed or cloud-based data pipelines Strong programming skills in a language of your choice, with a robust mental model of that language’s execution Enthusiasm and ability to use AI tools to complement your skills and boost your velocity Careful listener, strong communicator, and writes excellent tech specs Judgment and taste in prioritizing projects and selecting technical approaches Excited about biosecurity and pandemic prevention Nice to have Experience with workflow orchestrators like Nextflow, Flyte, Airflow, etc. Experience managing cloud resources via infrastructure as code Experience with tools and technologies we currently use, including Python, Rust, Nextflow, Terraform, or AWS Experience processing large scale sequencing data Logistics and benefits This is a full-time in-person role located in our Cambridge, MA office. For exceptional candidates, there may be flexibility on remote/hybrid work and starting salary. Depending on prior experience and demonstrated skills, this role may be hired at the Software Engineer or Senior Software Engineer level. Our employee benefits reflect our belief in investing to build the strongest possible team, in which everyone receives the trust and support they need to excel. Our benefits package includes: Comprehensive healthcare Comprehensive healthcare coverage, including health, dental & vision insurance, as well as a yearly mental health allowance for every employee. Flexible work schedule Flexible work hours; unlimited paid time off (PTO) for all employees; and minimum 12 weeks fully-paid parental leave. Development opportunities Generous professional development opportunities, including fully-paid conference sponsorships and a yearly development allowance for every employee. 401(k) Employer 401(k) match up to 4% of total salary. Excellent offices Superb working environments in our Kendall Square offices, including high-quality ergonomic office equipment, snacks, and daily catered lunches. Relocation & commuter suppor