Bioinformatician II Psychiatry
Brigham & Women's Hospital(BWH)

Boston, Massachusetts

Posted in Health and Safety


Job Info


Serve as a member of an interdisciplinary neuroimaging research group focused on understanding brain abnormalities and their role in neuropsychiatric disorders using state-of-the-art neuroimaging techniques. Develop novel neuroinformatics tools and new pipelines with an emphasis on version tracking and data provenance, high performance computing using Python programming, Bash scripting and Linux/Unix command line programs. Work closely with principal investigators to architect software models. Maintain and enhance existing image processing pipelines using tools like Luigi or Nipype. Apply various deep learning methods for automated brain masking and quality checking of an MRI using Keras or Pytorch package. Develop code that can be employed across a high-performance computing cluster and is suitable for parallel processing using LSF or SLURM. Develop web applications in HTML/JavaScript/CSS and deploy using Apache. Track changes, create pull requests and manage issues during software development. Test and evaluate a range of neuroimaging packages to determine their suitability for research goals. Program against various neuroimaging toolboxes such as FreeSurfer, FSL, Slicer, SPM & DIPY and medical research electronic data capture systems such as XNAT & REDCap. Write software documentation for medical researchers to follow. Assist researchers with software-related questions and problem solving. Attend research group meetings as required. Participate in writing manuscripts and grant proposals. Support data engineering efforts including database 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 such as Microsoft Azure, Google Cloud, or Amazon Web Services. Allocate and monitor high performance cluster resources among lab members. Build and maintain virtual machines for hosting web applications. Supervise a team of research assistants and a junior programmer, training them, assigning tasks, reviewing research assistants' data analysis outputs and programmers' codes, and overseeing the maintenance of source code repositories. Develop data visualization tools to monitor and visualize multi-site, multi-modal study data of human subjects

Qualifications
Must have Master's degree in Bioinformatics, Electrical Engineering, Computer Science or related field. 3 years of experience in the job offered or 3 years of bioinformatics or data analytics experience supporting medical research including maintaining and enhancing existing image processing pipelines, developing new pipelines including version tracking and data provenance, high performance computing, Python programming, Bash scripting and Linux/Unix command line programs. The stated experience must include 2 years working with the following: (1) pipeline building tools (Luigi orNipype); (2) deep learning packages (Keras or Pytorch); (3) high performance computing cluster job scheduling systems (LSF or SLURM); and (4) web development (JavaScript) and deployment (Apache).

Send resume to Shatasha Mayo, Talent Acquisition Partner, Human Resources, Mass General Brigham | Brigham Health,One Brigham Circle, 4th Floor, Boston, MA 02115. smayo1@partners.org

EEO Statement
EEO Statement:

Brigham and Women's Hospital is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, creed, sex, sexual orientation, gender identity, national origin, ancestry, age, veteran status, disability unrelated to job requirements, genetic information, military service, or other protected status.



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