Data Engineer

McLean Hospital is a comprehensive psychiatric hospital committed to providing easy access to superior quality, cost-effective mental health services in the Boston area, Massachusetts and beyond.  Since 1811, McLean Hospital has been a world leader in the treatment of mental illness and chemical dependency, research into the cause of mental illness and the training of generations of mental health care providers. McLean's multidisciplinary programs treat a broad range of psychiatric illnesses across the full continuum of care.

The Data Engineer will be part of a diverse interdisciplinary team at the Laboratory for Functional Neuroimaging and Bioinformatics with broad expertise spanning computer science, neuroscience, psychology, psychiatry, neuropsychology, cognitive neuroscience, neuroimaging, bioinformatics, biostatistics, epidemiology, and neurophysiology. Projects involve data processing and coordination for multisite data collection networks, as well as developing stratification tools to identify and validate biomarkers to predict outcome trajectories in individuals at high risk to develop psychosis.

The successful candidate will help develop, deploy, and maintain the bioinformatics infrastructure of several large projects being carried out by the lab. Our group is also actively developing new technologies to characterize brain structure and function, which has led to the design of state-of-the-art image analysis pipelines capable of robustly processing hundreds of neuroimaging datasets. The role of the engineer will be to maintain and enhance existing image processing pipelines and to develop new pipelines based on the latest research with an emphasis on version tracking, data provenance, and high-performance computing.

Principal Duties and Responsibilities:

Relevant activities include, but are not limited to the following:

• Design, implement, test, maintain and support applications to capture, manage, archive, and monitor multi-site, multi-modal study data. Applications may include but are not limited to study monitoring systems, data management systems, workflow execution and monitoring systems, interactive viewers, and reporting tools.
• Support web and application server configuration and deployment.
• Support data engineering efforts, including database and API design, data extraction/transformation/load, and data aggregation/integration.
• Containerize and deploy software and workflows on local high performance computing platforms and cloud computing infrastructure (AWS).
• Maintain and enhance existing image processing pipelines.
• Design new image processing pipelines, with an emphasis on version tracking, data provenance, and high-performance computing.
• Develop neuroinformatics tools to track data provenance and project management.
• Test and evaluate a range of neuroimaging packages to determine their suitability for research goals.
• Regular, direct interaction with neuroscientists from within and outside the team to assist them with data analysis using a range of methods including FSL, SPM, Slicer and other specialized tools.
• All McLean team members are expected to consistently demonstrate our values of integrity, compassion, respect, diversity, teamwork, excellence and innovation in their work activities and interactions.

Required:

• Bachelor's Degree in Computer Science, Mathematics, Physical Sciences, Engineering, or related field
• Experience with database management systems (e.g., SQL, PostgreSQL, MongoDB, CouchDB)
• Experience with Linux container engines (e.g., Docker, rkt) and container orchestration systems (e.g., Kubernetes)

Preferred:

• Master's Degree in Computer Science, Mathematics, Physical Sciences, Engineering, or related field
• Experience in neuroimaging software FSL, FreeSurfer, Slicer, DIPY, Nipype, Neurodocker, REDCap, XNAT

• Experience with JavaScript libraries for interactive data visualization (e.g. d3, Recharts, Charts.js).
• Experience with at least one web framework for building single-page web applications (e.g., React, Angular, Vue)
• Excellent programming skills in Python, Bash, MATLAB
• Superior Linux/Unix skills and comfort with command line programs - the ability to get new programs and packages running, overcoming hurdles as they arise, is particularly helpful.
• Familiarity with standard software evolution method-version controlling (Git), pull requests, code reviews, issue and release management
• Ability to work in an interdisciplinary, diverse, and international team in a highly collaborative and intellectually challenging environment.
• Excellent oral and written communication skills
• Basic knowledge of neuroscience and neuroanatomy.
• Understanding of structural, diffusion, and functional Magnetic Resonance Imaging.
• Familiarity with C/C programming
• All employees must possess basic computer skills to use a variety of electronic or online systems for communication, clinical and administrative purposes.