Research Software Engineer

Harvard University; Boston (MA); Hybrid; USD 120,000 - 170,000; Full time

Benefits offered by this job

Generous paid time off

Medical, dental, and vision insurance

Tuition assistance and reimbursement

Commuter benefits and campus perks

Job summary

Harvard University’s HIDIVE Lab at the Department of Biomedical Informatics seeks a Research Software Engineer to lead software projects and develop open-source tools for visualization and analysis of genomic, single-cell, and spatial omics data.

You will collaborate across national and international consortia, mentor trainees, and publish results while contributing to cloud and on-premise deployment and data standards. This role supports hybrid work and offers a comprehensive benefits package.

Qualifications

• Seven years of post-secondary education or relevant work experience.
• Doctoral degree strongly preferred in biomedical informatics, CS, computational biology, data science, or related field.
• 5+ years in software engineering with web app focus.
• 5+ years in data analysis and visualization of single-cell and spatial biology data.
• 5+ years in biomedical data research and large-scale collaborative projects.
• 3+ years in open-source software development and community building.

Responsibilities

• Design, implement, and maintain open-source research software tools for visualization and analysis of omics data.
• Lead one or more software projects with clear strategy and roadmaps.
• Maintain code quality with testing, CI, documentation, and release management.

Skills

Python

R

Open source software development

Data visualization

Web applications

Biomedical data visualization

Grant writing

Mentoring

Education

Doctoral degree in biomedical informatics or related field

Tools

HiGlass

Vitessce

Gosling

HuBMAP Data Portal UI

Job description

Company Description

By working at Harvard University, you join a vibrant community that advances Harvard's world-changing mission in meaningful ways, inspires innovation and collaboration, and builds skills and expertise. We are dedicated to creating a diverse and welcoming environment where everyone can thrive.

Harvard Medical School's mission is to nurture a diverse, inclusive community dedicated to alleviating suffering and improving health and well-being for all through excellence in teaching and learning, discovery and scholarship, and service and leadership.

You’ll be at the heart of biomedical discovery, education, and innovation, working alongside world-renowned faculty and a community dedicated to improving human health. This is more than a job - it’s an opportunity to shape the future of medicine.

About the Department of Biomedical Informatics

Our Lab

Join our team of researchers, engineers, and designers to shape a future in which humans and AI collaborate to solve the most challenging biological and medical problems!

The HIDIVE Lab in the Department of Biomedical Informatics at Harvard Medical School is conducting research at the interface human and artificial intelligence. We create methods and tools that enable humans and machines alike to interact with and generate insights from biomedical data. In our work, we combine state-of-the-art biomedical informatics, data visualization, and AI/ML techniques across the full spectrum of biomedical data. An overview of recent publications of the lab can be found on Google Scholar https://scholar.google.com/citations?hl=en&user=YEcBVFAAAAAJ&view_op=list_works&sortby=pubdate .

We value diverse viewpoints, creative thinking, and bold initiative in a highly collaborative and interdisciplinary work environment. The HIDIVE Lab has an international reputation for creating high impact data visualization tools and we are driven to solve the most challenging design and engineering problems where biomedical data, humans, and AI meet. We would love to have you on our team!

Our Research

We are currently looking for a Research Software Engineer who wants to contribute to our mission by leading software projects in one or more of the following areas:

• Generative AI for visual exploration of biomedical data
• Mixed Reality for 2D and 3D tissue data visualization in spatial biology
• Multimodal spatial and single-cell data visualization
• 2D and 3D bioimaging data visualization
• Data analysis and data management infrastructure for biomedical data visualization

Our Resources

The HIDIVE Lab participates in large-scale collaborative projects such as:

• NIH Human Biomolecular Atlas Program (HuBMAP): https://hubmapconsortium.org/
• NIH Cellular Senescence Network (SenNet): https://sennetconsortium.org/
• NIH Kidney Precision Medicine Network (KPMP): https://www.kpmp.org/
• NIH Common Fund Data Ecosystem (CFDE): https://commonfund.nih.gov/dataecosystem
• APRA-H Biomedical Data Fabric (BDF, and Pediatric Care eXpansion - PCX): https://arpa-h.gov/explore-funding/programs/arpa-h-bdf-toolbox
• Human Cell Atlas (HCA): https://www.humancellatlas.org/
• NIH 4D Nucleome Consortium (4DN): https://4dnucleome.org/

Through these projects, we have access to a large number of data sets across many data modalities as well as large user audiences and collaborators who are leading experts in their biomedical domains. We are also working with many individual collaborators at Harvard and beyond, who bring their computational, data science, and biomedical expertise to our projects.

Our work also benefits from multiple research software products (e.g., HiGlass, Vitessce, Gosling, HuBMAP Data Portal User Interface, etc.) that the HIDIVE Lab has developed and maintains through a team of engineers and designers. These products are used by individual scientists, consortia, and companies all over the world and can serve as a framework to implement and disseminate the outcomes of our research.

Job Description

As a Research Software Engineer in the lab, you will take an engineering and research leadership role and be in charge of one or more software projects. This will include:

• Software Development: Design, implement, and maintain open-source research software tools for the visualization and analysis of genomic, single-cell, and spatial omics data.
• Project Leadership: Take engineering and research ownership of one or more software projects, developing and executing project strategy and roadmaps.
• Software Maintenance and Quality: Establish and uphold engineering best practices, including code review, testing, continuous integration, documentation, and release management, to ensure long-term sustainability of lab software.
• Research and Publication: Lead the writing of peer-reviewed publications describing novel methods, tools, and applications, and present work at scientific conferences.
• Community Building and Outreach: Grow and support open-source user and developer communities through documentation, tutorials, workshops, issue triage, and engagement with external contributors.
• Collaboration: Work with collaborators in national and international research consortia and with domain scientists to gather requirements, integrate tools into their workflows, and deliver on joint milestones.
• User Research: Conduct user studies and gather feedback from domain scientists to inform tool design and prioritization.
• Data Standards: Contribute to the development and adoption of community data standards and file formats for genomic and spatial omics data.
• Funding Acquisition: Contribute to the preparation of grant proposals and pursue industry sponsorship and other funding opportunities to sustain and expand software projects.
• Mentorship: Mentor and supervise trainees, including interns, Masters and PhD students, as well as staff members, on software engineering practices and research methods.
• Teaching: Participate in teaching activities, such as guest lectures, course modules, or training sessions.
• Infrastructure and Deployment: In collaboration with the engineering team, deploy, monitor, and maintain cloud-based and on-premise services supporting lab software and data portals.

Qualifications

Basic Qualifications:

• Minimum of seven years’ post-secondary education or relevant work experience.

Additional Qualifications and Skills:

• Doctoral degree in biomedical informatics, computer science, computational biology, data science or a related field- strongly preferred.
• 5+ years software engineering experience with focus on web applications.
• 5+ years experience in data analysis and visualization of single-cell and spatial biology data.
• 5+ years biomedical data research experience.
• 5+ years experience working in large scale collaborative research projects in academic/publicly funded research, track record of leading major academic research software projects.
• 3+ years experience in open source software development and community building.
• 3+ years experience in training and community outreach.
• 1+ years experience in mentoring trainees and staff.
• Proven success in publishing in bioinformatics and computational biology venues.
• Data visualization research experience.
• Python and R software development.
• Grant writing skills.

Additional Information

• Term: This is a one-yearterm position from the date of hire, with the possibility of extension, contingent upon work performance and continued funding to support the position.
• Standard Hours/Schedule: 35 hours per week
• Visa Sponsorship Information: Harvard University is unable to provide visa sponsorship for this position.
• Pre-Employment Screening: Identity
• Staying Informed About Your Application: Due to the high volume of applications, we may not always be able to reach out right away, but you can track your status anytime through the Careers@Harvard portal.

Work Format Details

This position has been determined by school or unit leaders that some of the duties and responsibilities can be effectively performed at a non-Harvard location. The work schedule and location will be set by the department at its discretion and based upon operational needs. When not working at a Harvard or Harvard-designated location, employees in hybrid positions must work in a Harvard registered state in compliance with the University’s Policy on Employment Outside of Massachusetts. Additional details will be discussed during the interview process. Certain visa types and funding sources may limit work location. Individuals must meet work location sponsorship requirements prior to employment.

Salary Grade and Ranges

This position is salary grade level 059. Please visit Harvard's Salary Ranges to view the corresponding salary range and related information.

Benefits

Harvard offers a comprehensive benefits package that is designed to support a healthy work-life balance and your physical, mental and financial wellbeing. Because here, you are what matters. Our benefits include, but are not limited to:

• Generous paid time off including parental leave
• Medical, dental, and vision health insurance coverage starting on day one
• Retirement plans with university contributions
• Wellbeing and mental health resources
• Support for families and caregivers
• Professional development opportunities including tuition assistance and reimbursement
• Commuter benefits, discounts and campus perks

Learn more about these and additional benefits on our Benefits & Wellbeing Page.

EEO/Non-Discrimination Commitment Statement

Harvard University is committed to equal opportunity and non-discrimination. We seek talent from all parts of society and the world, and we strive to ensure everyone at Harvard thrives. Our differences help our community advance Harvard's academic purposes.

Harvard has an equal employment opportunity policy that outlines our commitment to prohibiting discrimination on the basis of race, ethnicity, color, national origin, sex, sexual orientation, gender identity, veteran status, religion, disability, or any other characteristic protected by law or identified in the university's non-discrimination policy. Harvard's equal employment opportunity policy and non-discrimination policy help all community members participate fully in work and campus life free from harassment and discrimination.