Software Engineer

Software engineer to lead software development of the “Neurobooth” project, which is an effort to perform large scale digital phenotyping inside the Mass General neurology clinic. With funding from industry, government, and academic institutions, we have created a booth that is equipped with an array of devices, including consumer and industrial grade cameras, eye trackers, microphones, wearable sensors, and other sensors for physiological measurement. Patients perform motor and cognitive tasks inside the booth while collecting synchronized data from the devices. Sensor data are integrated with clinical data, organized in a database, and routed to a computing cluster for analysis. Data visualizations and summaries are generated in real-time to enable sharing of information with clinicians and patients in the clinic. This long-term project will generate the first dataset of its kind to support training of machine learning models and creation of tools to detect early signs of disease, precisely measure disease for clinical trials, and understand molecular and systems-level underpinnings of behavior in neurological diseases.

The role requires an experienced and multitalented software engineer (with hardware integration experience) to ensure that the custom built Python-based operating system that controls all aspects of Neurobooth is highly robust, uses software development best practices, and enables any team in the world to use and build upon the system as an open source project.

This is a part-time position expected to be around 20 hours/week, with flexibility. To be discussed during the recruitment process.

This position involves a wide range of responsibilities, including:

• Managing and organizing software and hardware development plans for Neurobooth in an Agile framework
• Maintaining both production and development software environments, collaborating closely with computer scientist postdoctoral fellows in the group. Support deployment and maintenance of a second version of the system at a clinical research facility in the Charlestown Navy Yard (i.e., “Neuroroom”).
• Incorporating software best practices including continuous integration and error handling
• Creation of automatic tests to ensure the network and hardware are running properly
• Creation of automatic tests to support incorporation of new features
• Improvement of real-time time series visualizations and to help ensure data quality at collection time
• Development of time series analyses and sync tests to ensure devices are collecting data at the specified sample rates and to evaluate data synchronization across devices
• Implement improvements of the GUI for running a Neurobooth session
• Reorganization of code base as necessary to avoid duplication of code
• Careful documentation of the code base
• Create and update documentation for the network architecture, hardware architecture, data flow, and database schema
• Management of computers, devices and other connected hardware
• Integration of new devices and sensors into the Neurobooth system
• Creation of new behavioral tasks to run in the booth using the PsychoPy toolkit
• Managing and further developing the PostgreSQL database and API that specifies Neurobooth session parameters (e.g., study, task, device), ingests clinical and survey data from REDCap, and logs session, task, and sensor files generated in Neurobooth for easy query and analysis
• Leading next steps with moving the database to Google Cloud Platform and the Terra data platform created at the Broad Institute
• Build upon automatic data flow processes to ensure robust data transfers and backups
• There are additional software development, data visualization, and data analysis opportunities depending on the individual’s interests

• Proficiency with Python, SQL, and Git required.
• Demonstrated ability in developing software applications that control hardware over a network for time series data acquisition.
• Expertise in relational database management and ETL for batch processing
• Facility with "tools of the trade", e.g., Unix system administration, shell scripting, building and deployment tools, version control.
• Experience with time series data visualization and analysis
• Experience with cloud computing.
• Familiarity with use of lab streaming layer (LSL) and creating behavioral tasks using PsychoPy is preferred.
• Proven ability to meet deadlines and work cooperatively in a collaborative team.

Bachelor’s degree required. Master’s degree in Computer Science or related field preferred.

3+ years of experience working in software development.

1+ years of experience developing integrated hardware and software systems.

The software engineer will work within a team of data scientists, clinical research coordinators, and physician-scientist neurologists. Work will be performed in the Laboratory for Deep Neurophenotyping (located in downtown Boston) and the Alzheimer’s Clinical and Translational Research Unit, in collaboration with other academic and industry partners in the Greater Boston area.