- Division: SecureBio Detection
- Start date: as soon as possible
- Status: full-time SecureBio employee
- Approximate compensation: $165,000 - $195,000
- Visa sponsorship: not available
- Work location: in-person in Cambridge, MA strongly preferred
Role Overview
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 build out and strengthen the pipelines behind it. This is a broad software engineering role: you’ll develop new pipeline capabilities, improve the performance and accuracy of our detection algorithms, build internal tooling, and shape how we model and store our data. Prior experience with biology or bioinformatics is not required.
Responsibilities
- Pipeline development: design and build new pipeline features and stages, from prototype to production.
- Pipeline performance: benchmark pipelines, identify bottlenecks, and implement optimizations.
- Pipeline accuracy: improve the sensitivity and specificity of our detection algorithms.
- Data modeling and databases: design schemas and data models that keep our growing volume of sequencing data queryable and maintainable.
- Internal tooling: build tools and abstractions that make the team faster and the pipelines easier to work with.
- AI acceleration: stay current with rapid AI progress and creatively use AI tools to accelerate your work.
Qualifications
Must have
- 2+ years of professional experience in software engineering or a related field
- Strong software engineering fundamentals: reliable, maintainable code and sound software design
- A rigorous approach to testing and reliability – you write well-tested code and think carefully about failure modes
- 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
- Proficiency with performance patterns across the full stack, e.g. memory access patterns, networking, and algorithm asymptotic complexity
- 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.
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 support
Free commuter benefits up to $250/month, plus a generous relocation allowance for employees who move to the Boston area.
Referral bonus
We offer a referral bonus of up to $6,000 to individuals who refer successful candidates for this position:
To receive these bonuses, we must reasonably believe that you were responsible for referring the candidate to us (e.g. due to you introducing them to us when we didn’t previously know them, or them mentioning you on their application as the reason they heard about the position).
- If you refer a candidate that we invite to an in-person work trial, you will receive $1,200;
- If the candidate accepts a job offer from us, you will receive a further $4,800, for a total of $6,000.
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