Software engineer for cloud-based image management and visualization

Harvard Program in Therapeutic Science · Boston, Massachusetts
Department Harvard Program in Therapeutic Science
Employment Type Full-Time
Minimum Experience Mid-level

Software engineer for cloud-based image management and visualization


About the position

We seek a senior software engineer to join a team of professional scientists and programmers revolutionizing how cancers are diagnosed and treated. The engineer will develop key software components for web-based cancer atlases that use cloud technologies, machine learning, and human-machine interfaces to integrate high dimensional imaging and clinical data. The project involves scientists and engineers from Harvard, Dana Farber Cancer Institute, MIT, the Broad Institute, and European universities, and companies developing new tissue imaging technologies, and is part of a multi-institution initiative funded by the National Cancer Institute (NCI). More information about the project, including links to open source code repositories, literature citations, and an early version of an atlas-style imaging data browser can be found at https://www.tissue-atlas.org/.

 

The ideal applicant will be a software engineer with a strong background in cloud technologies, significant experience with Python programming, and an interest in advancing human health in an entrepreneurial academic setting. The candidate must have the capacity to conceptualize the overall design of complex software systems and contribute to and manage their implementation. The candidate must be self-directed while also working well as part of a small team. Programming work will include individual contributions, collaboration with junior engineers, and ”customer” meetings with in-house computational biology and wet-bench researchers. Candidates are encouraged to attend scientific and technology conferences and will participate in the preparation of scientific manuscripts and reports.

 

Responsibilities

  • Work with image and data visualization experts in the LSP to develop and deploy Cancer Atlases: Fundamentally new approaches to visualizing, managing, and analyzing image and molecular data from human cancer biopsies
  • Take a lead role in the continued development of a cloud-based platform (deployed on Amazon Web Services) for imaging informatics as described at https://github.com/sorgerlab/minerva-infrastructure/
  • Develop cloud-based modular tools that support the Atlas projects and can be reused in other contexts for future projects
  • Manage all code in Git and write tests and documentation for all code
  • Release all code as open source and assist the team with support tasks such as issue management and review of external contributions
  • Participate in code review sessions with the team
  • Advise and support junior software engineers
  • Develop collaborative peer relationships with engineers at other NCI-funded research centers
  • Present your work in internal LSP lab meetings and, optionally, at national and international scientific conferences and participate in internal and external meetings around campus
  • Assist in the preparation and publication of peer-reviewed scientific manuscripts
  • Work directly with the LSP Director of Software Engineering and the faculty director of the LSP


Mandatory qualifications

  • MSc in computer science, bioinformatics, or related discipline, or substantial experience in software engineering
  • Extensive Python programming experience, including performance tuning, debugging, and familiarity with scientific packages such as numpy and scikit-learn
  • 6+ months of hands-on experience participating in team-based open source software projects
  • Experience in cloud technologies with an emphasis on Amazon Web Services.
  • Experience with Docker or other containerization technologies
  • Experience using Git or an equivalent distributed source control system
  • Proven ability to work well with and support junior colleagues
  • Excellent oral and written communication skills

 

Desired qualifications

  • Proficiency with Java and JavaScript
  • Experience with image processing or bioinformatics
  • Experience with microscope imaging technologies
  • Experience with management of large-scale datasets


This position is available with a partially or fully remote option for applicants living in or planning to relocate to the following U.S. states: Maine, New Hampshire, Vermont, Massachusetts, Rhode Island, Connecticut, New York, Maryland, California.

 

About the Laboratory of Systems Pharmacology

The Laboratory of Systems Pharmacology (LSP) is a highly collaborative, multidisciplinary research and education program located in the center of Harvard Medical School (HMS). The LSP engages in a wide variety of research projects focused on cancer, Alzheimer’s disease, chronic pain, and infectious disease. Career bench scientists, software and instrumentation engineers, and data analysts play essential roles in these projects. The LSP has a very active software team that oversees the development and implementation of open-source tools for data integration and analysis, image management, machine learning, and visualization.

 

The LSP is a component of the Harvard Program in Therapeutic Science (HiTS - http://hits.harvard.edu), which aims to reinvent the fundamental science underlying the development of new medicines and their use in individual patients. LSP staff, faculty, administrators, and students represent a wide range of ages, races, interests, and backgrounds come together in pursuit of common goal of fundamentally improving human health. Harvard is an Affirmative Action/Equal Opportunity Employer and applications from women and persons of color are strongly encouraged.

 

Former LSP members are now faculty members in US, Europe, and Asian universities, lead core facilities or interdisciplinary projects at leading academic research institutions, have started software and biotech companies using the lab’s technologies, and have assumed leadership positions in the pharmaceutical industry.


Compensation and Benefits

  • Salaries are based on level of experience and competitive with similar positions in research institutions
  • Exceptional set of Harvard-provided health and welfare benefits (https://hr.harvard.edu/health-welfare-benefits)
  • Signing bonus
  • New desktop and/or laptop computer and all desired developer tools
  • Either remote, hybrid on or-site work options with desk and office space in the LSP as needed in the historic Armenise or Warren Alpert Buildings on the HMS Quadrangle
  • Opportunity to attend two conferences or scientific meetings per year in the US or Europe.
  • Extensive opportunities to interact and network with programmers and cancer biologists developing next-generation approaches to health care.

 

How to apply

Please submit a cover letter, a current CV and two references via the Bamboo HR portal (https://hitsedu.bamboohr.com/). The cover letter must highlight your past open-source software contributions and include links to GitHub, GitLab, or other public repositories as appropriate. Please include examples of communication with other developers and users (e.g., via GitHub Issues, Stack Overflow, developer forums, etc.). Promising candidates will be contacted for a Zoom interview and either remote or in-person meetings with lab members. The LSP currently operates a hybrid work model with scientific staff on-site 3-5 days per week depending on job function (and subject to change based on Harvard, Federal and State pandemic policy).

Thank You

Your application was submitted successfully.

  • Location
    Boston, Massachusetts
  • Department
    Harvard Program in Therapeutic Science
  • Employment Type
    Full-Time
  • Minimum Experience
    Mid-level