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Software Engineer - Refinery Platform

Posted on 31 July 2019

We are looking to hire a Software Engineer to join the Gehlenborg Lab to participate in the development of the Refinery Platform for data visualization, management, and analysis, as well as the Harvard Stem Cell Commons.

The Gehlenborg lab in the Department of Biomedical Informatics is part of a vibrant community of scientists, physicians, and engineers whose goal is to advance the boundaries of knowledge. The Department leads the development of computational and informatics techniques to address pertinent challenges in modern biological sciences and medicine. The Department’s faculty conduct research at the intersection of biomedicine and information sciences, including bioinformatics, functional genomics, translational medicine, and clinical knowledge management. Based on the Harvard Medical School Longwood Campus, it provides a rich scientific environment, with many seminar series and invited speakers of the highest caliber.


The Gehlenborg Lab in the Department of Biomedical Informatics at Harvard Medical School is leading the development of the Refinery Platform, an innovative open-source, web-based software environment for the management, analysis, and visualization of epigenomic and genomic data.

As part of an initiative with the Harvard Stem Cell Institute, the Gehlenborg Lab is looking for an experienced and enthusiastic software developer to participate in extending Refinery Platform for the Harvard Stem Cell Commons. A major goal of the system is to provide a shared environment to enable users to compare stem cell data across different laboratories, experimental platforms, organisms, and cell types.

You will be working as part of a small, dynamic team in a modern, open-source development environment. As a team, we strive to make our tools readily usable by biologists and work closely with them. This is a great opportunity to be involved in cutting-edge stem cell research and the open-source bioinformatics community. This position is funded for one year from date of hire, with the expectation of renewal.

Our ideal candidate has experience in backend web application development with a focus on designing, developing and maintaining production software systems in data-intensive settings, ideally for scientific applications. The developer must be able to adapt to changing specifications and priorities, be willing to take initiative and ownership of their work, and learn. Must be self-motivated, self-starter, and able to manage own time.

The software developer should be comfortable with and be experienced in working on server-side components (including compute clusters and/or clouds) and deployment, as well as modern software engineering practices such as automated testing and continuous integration/deployment.

Furthermore, the developer must be proficient in Django or other web frameworks and have a working knowledge of SQL databases. Expertise in REST API design and implementation is expected and experience in HTML5, JavaScript, and UI frameworks such as AngularJS or Bootstrap is desirable.

Basic Requirements

BSc in Computer Science or a related field and 2 or more years related experience or 4 or more years of professional experience in web application development with tools such as Python or other web frameworks (e.g., Django), Apache, SQL (e.g., PostgreSQL), Git, automated testing. Proficiency in AWS or another major cloud platform.

Additional Requirements

MSc in Bioinformatics, Computer Science or a related field and 5 years of work experience. Familiarity with bioinformatics, Galaxy, Docker, Vagrant, Solr/Elasticsearch, Celery, REST API design and implementation, Bootstrap, continuous integration/deployment, Terraform, as well as understanding of configuration management tools (e.g. Puppet, Ansible or Chef) and JavaScript frameworks (e.g., AngularJS) will be helpful.

How to Apply

Please follow the instructions on the Harvard Careers website.

Harvard Medical School is an Equal Opportunity/Affirmative Action Employer. Women and minorities are especially encouraged to apply.