Senior Software Engineer – Biomedical Informatics

Axle is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations nationally and abroad. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques to empower decision-making and accelerate research discoveries. We work with some of the top research organizations and facilities in the country including multiple institutes at the National Institutes of Health (NIH).

Benefits We Offer:

• 100% Medical, Dental & Vision Coverage for Employees
• Paid Time Off and Paid Holidays
• 401K match up to 5%
• Educational Benefits for Career Growth
• Employee Referral Bonus
• Flexible Spending Accounts:
  • Healthcare (FSA)
  • Parking Reimbursement Account (PRK)
  • Dependent Care Assistant Program (DCAP)
  • Transportation Reimbursement Account (TRN)

Axle is seeking a Senior Software Engineer – Biomedical Informatics to join our vibrant team at the National Institutes of Health (NIH) supporting the National Center for Advancing Translational Sciences (NCATS) located in Rockville, MD.

We are seeking a Senior Software Engineer with deep experience in scientific computing and biomedical informatics to lead the development and maintenance of software systems that support translational research. This role involves architecting and operating Python-based applications, managing cloud infrastructure, and working with biomedical data standards and machine learning models.

You will work across multiple project streams as part of a cross-functional team that includes data scientists, researchers, and other engineers. A key aspect of this role is partnering directly with subject matter experts — scientists and researchers who understand the problem domain but may not have a technical background — to elicit requirements, translate research needs into well-defined technical solutions, and ensure that delivered software meets their real-world needs. The role requires a seasoned, self-directed engineer who can make sound architectural decisions, mentor junior team members, take ownership of technical components end-to-end, and deliver iteratively in a collaborative research environment.

Key Responsibilities

• Architect, develop, and maintain Python-based scientific software, including client/server libraries, CLI tools, and containerized applications.
• Lead technical design decisions and establish best practices for code quality, testing, and deployment.
• Provision, deploy, monitor, and troubleshoot cloud services on AWS, including managing IAM roles, deployment pipelines, and S3 storage.
• Work with embedding models and vector databases to support NLP and semantic search capabilities.
• Design and maintain OMOP-compliant PostgreSQL databases, including vocabulary management and incremental data updates.
• Develop and maintain data migration and extraction scripts, with appropriate logging and verification for completeness.
• Conduct integration testing with external systems and evaluate model performance against large-scale datasets.
• Drive documentation, testing, and CI/CD workflows to support reliable software delivery.
• Engage directly with non-technical subject matter experts to gather requirements, clarify goals, and validate that delivered solutions align with research objectives.
• Translate high-level research needs into actionable technical specifications and development plans.
• Mentor junior engineers and contribute to a culture of technical excellence.

• Participate in and help facilitate standups, sprint planning, and cross-team review meetings across multiple project streams.

Required Skills & Qualifications

• 5+ years of professional experience in software development.
• Proficiency in Python for application development, scripting, and tooling.
• Demonstrated experience with machine learning models.
• Demonstrated experience making architectural decisions and owning technical direction for software projects.
• Experience with AWS (IAM, S3, deployment, general infrastructure management).
• Experience with PostgreSQL and relational database design.
• Experience with Docker and containerization workflows.
• Strong command of Linux development environments.
• Experience with Git/GitHub workflows, including branching, pull requests, and code review practices.

• Proven ability to work independently, prioritize across concurrent workstreams, and drive projects to completion with minimal oversight.

Preferred Qualifications

• Experience with NLP.
• Experience with GPU computing (CUDA/NVIDIA).
• Familiarity with the OMOP Common Data Model or biomedical ontologies and vocabularies.
• Experience working with healthcare records, patient data, or clinical datasets.
• Experience with PostgreSQL extensions such as pgvector for vector similarity search.
• Background in biomedical informatics, translational research, or health sciences.

• Familiarity with Jira or similar project management tools.

Interpersonal Skills

• Strong written and verbal communication skills, including the ability to convey technical concepts to non-technical collaborators and translate domain expertise into software requirements.
• Skilled at requirements elicitation — able to ask the right questions, listen actively, and bridge the gap between what subject matter experts need and what engineering can deliver.
• Ability to work effectively across multiple teams and project streams with different leads, priorities, and cadences.
• Comfortable operating in a large, cross-functional team environment where coordination and alignment are essential.
• Proactive in communicating progress, raising blockers, and seeking input from teammates and stakeholders.
• Tactful and professional when engaging with clients and external partners; able to navigate sensitive situations and escalate appropriately.

• Receptive to feedback and committed to iterative improvement.

What We Emphasize

• Proactive communication and early delivery over perfection
• Ownership of well-scoped technical components with clear rationale for decisions
• Self-driven initiative in managing code quality, versioning, and task completion
• Willingness to research and adopt new technologies and libraries

• Collaboration and mentorship within a multidisciplinary team

Disclaimer: The above description is meant to illustrate the general nature of work and level of effort being performed by individuals assigned to this position or job description. This is not restricted as a complete list of all skills, responsibilities, duties, and/or assignments required. Individuals may be required to perform duties outside of their position, job description or responsibilities as needed.

The diversity of Axle's employees is a tremendous asset. We are firmly committed to providing equal opportunity in all aspects of employment and will not tolerate any illegal discrimination or harassment based on age, race, gender, religion, national origin, disability, marital status, covered veteran status, sexual orientation, status with respect to public assistance, and other characteristics protected under state, federal, or local law and to deter those who aid, abet, or induce discrimination or coerce others to discriminate.

Accessibility: If you need an accommodation as part of the employment process please contact: careers@axleinfo.com

This role has a market-competitive salary with an anticipated base compensation range listed below. Actual salaries will vary depending on a candidate's experience, qualifications, skills, and location.