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Senior Software Engineer, Scientific Computing Software

Howard Hughes Medical Institute (HHMI)
United States, Maryland, Chevy Chase
4000 Jones Bridge Road (Show on map)
April 13, 2023
Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account.

Janelia Research Campus is a pioneering research center in Ashburn, Virginia, where scientists pursue fundamental questions in neuroscience and imaging. The Howard Hughes Medical Institute (HHMI) launched Janelia in 2006, establishing an intellectually distinctive environment for scientists to do creative, collaborative, hands-on work. Our integrated teams of biologists, computational scientists, and tool-builders pursue a small number of scientific questions with potential for transformative impact. We share our methods, results, and tools with the scientific community. It is a uniquely innovative and collaborative atmosphere that reflects HHMI's reputation for excellence.


We are seeking a talented and motivated individual to join the Scientific Computing Software as a Senior Software Engineer. The successful candidate can write complex code (e.g. Java, Python) in a scientific environment and has experience developing software using complex APIs. The candidate will work closely with scientists and learn about their goals and workflows, translating them into high-quality software that accelerates science. They must be able to implement mathematical concepts as code, using state-of-the-art libraries such as numpy, ImgLib2, and PyTorch.

The ideal candidate thrives in a fast-paced research environment with constantly evolving requirements, enjoys writing maintainable software, and feels pride and ownership for any code they deliver. This role comes with the opportunity to take part in all aspects of the software development lifecycle on a diverse range of projects supporting both labs at Janelia and the wider community through projects such as , , and .


  • Collaborate with scientists, scientific programmers, and a team of software engineers to build world-class scientific software

  • Translate computational research methods into well-factored, maintainable code

  • Create and maintain software capable of running on local workstations, an HPC cluster, and in the cloud

  • Follow industry best practices for unit testing, documentation, CI/CD, DevOps, and MLOps

  • Engage with the software community at Janelia to learn and share knowledge about scientific software development


  • Bachelors or Masters in computer science, bioinformatics, or relevant field

  • 3+ years of experience in software engineering

  • Ability to understand scientific problems related to biomedical research

  • Demonstrated proficiency in Python and/or Java programming

  • Experience with Linux and bash scripting

  • Experience with containerization technologies such as Docker or Singularity

Preferred Qualifications:

  • Experience with Nextflow, Snakemake, or other workflow systems

  • Experience with distributed computing frameworks such as Dask, Spark, or Ray

  • Experience with cloud technologies, especially AWS

  • Knowledge of machine learning fundamentals

If you are excited about a specific open-source project that you have contributed to, please include it in your application so we can discuss code together.

Physical Requirements:

Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet).

Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.

Please Note:

This job description sets forth the job's principal duties, responsibilities, and requirements; it should not be construed as an exhaustive statement, however. Unless they begin with the word "may," the Essential Duties and Responsibilities described above are "essential functions" of the job, as defined by the Americans with Disabilities Act.

Compensation and Benefits

Our employees are compensated from a total rewards perspective in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our site to learn more.

Compensation Range

$85,690.00 (minimum) - $107,200.00 (midpoint) - $139,260.00 (maximum)

Pay Type:


HHMI's salary structure is developed based on relevant job market data. HHMI considers a candidate's education, previous experiences, knowledge, skills and abilities, as well as internal equity when making job offers. Typically, a new hire for this position in this location is compensated between the minimum and the midpoint of the salary range.