Senior Software Engineer/Founding Member

Job Title

Software Engineer

Location

Cambridge, Massachusetts, United States, 02142

Job Description

The Software Engineer is a senior technical contributor responsible for designing, scaling, and optimizing high-throughput batch processing workflows that power FGI's genomic diagnostics platform. This role requires deep experience building large data ingestion pipelines, processing raw scientific datasets, and integrating analytical tooling in cloud environments. Candidates must bring a strong academic foundation and a proven history of delivering production-grade systems in biotech, diagnostics, genomics, or similarly data-intensive scientific domains.

Technologies Used:

• Languages: Python, R, Bash, Java, PyTorch/Pyro
• Frameworks: WDL, Cromwell, GCP Batch
• Infrastructure: GCP, S3, Docker, CI/CD pipelines
• Data Tools: PostgreSQL, Pandas, cloud-based data lakes
• Monitoring: Prometheus, Grafana
• Interfaces: Command-line and configuration-based systems (GUI optional)

Education and Experience:

Bachelor's degree in Computer Science, Bioinformatics, or a related field required; Master's degree preferred. Experience working within a diagnostic, healthcare, or life sciences organization is highly desirable.

Requirements:

Software Design and Development:

• Lead the development and optimization of large-scale batch data processing workflows for raw genomic or scientific datasets.
• Design and maintain distributed backend services and workflow orchestration systems to handle complex analytical pipelines.
• Architect and own high-performance cloud infrastructure supporting large data volumes and sequential processing (GCP strongly preferred).
• Build tools for validating, transforming, and preparing scientific datasets for downstream analysis.
• Ensure pipeline reproducibility, auditability, and robustness under strict regulatory and data privacy requirements.

Collaboration:

• Collaborate closely with bioinformatics and scientists to translate analytical workflows into scalable engineering solutions.
• Participate in design reviews focused on workflow optimization, throughput, and computational efficiency.

Minimum Qualifications (Knowledge, Skills, and Abilities):

• 6+ years of professional software engineering experience with a significant focus on data processing, scientific computing, or workflow/pipeline development.
• Demonstrated experience leading or owning complex pipeline architecture (not just contributing).
• Strong background in large batch data processing, HPC-style workflows, or scientific/analytical pipelines.
• Master's degree required in Computer Science, Bioinformatics, Computational Biology, or related field. A Bachelor's may be considered only with exceptional, directly relevant scientific computing experience.
• Experience in biotech, diagnostics, genomics, or a closely related scientific domain is required.
• Proficiency in Python and modern workflow frameworks (WDL, Nextflow, Cromwell, etc.).
• Proven cloud experience (GCP strongly preferred).
• Strong understanding of security, privacy, and handling of PHI.

Preferred Qualifications:

• 7–10+ years of experience building and scaling scientific workflows or distributed data pipelines.
• Direct experience processing genomic, imaging, or other scientific raw data.
• Proven ability to optimize end-to-end workflows for speed, cost, and reliability.
• Experience with workflow orchestration, high-throughput computer systems, and scientific reproducibility tools.

Benefits:

• Compensation Salary Range: $165K–$190K per year. Competitive salary and benefits package commensurate with experience. Equity participation through FGI's upcoming partner program.
• Flexible remote or hybrid work options (Boston-based collaboration preferred).
• Mission-driven culture with strong emphasis on transparency, innovation, and collaboration.

Work Environment & Physical Requirements:

• Work Environment: This is a fully remote position. The employee must have a reliable internet connection and a suitable workspace.
• Physical Requirements: Regular use of a computer, including extended periods of screen time. Occasional participation in virtual meetings.

We are an Equal Employment Opportunity Employer and we do not discriminate on the basis of race or ethnicity, religion, sex, national origin, age, veteran disability or genetic information or any other reason prohibited by law.