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Data Engineer - Multimodal Data Integration

Allen Institute
Times Square, WA
Closing date
May 29, 2023
Data Engineer I - Multimodal Data Integration

The mission of the AllenInstitute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the AllenInstitute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

The mission of the Allen Institute for Brain Science is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through integration of experiments, modeling and theory.

As part of the NIH BRAIN Initiative Cell Atlas Network, the Allen Institute is helping to lead a major new international consortium effort to create a comprehensive cell atlas of the human and closely related non-human primate brain. This project aims to make the most detailed map of the human brain ever produced, linking cellular and molecular phenotypes to brain imaging and functional architecture. To tackle this ambitious goal, we are seeking talented and highly motivated individuals to help create these atlases and help to make them transformative for neuroscience and biomedical research through open data sharing. The atlas will be based on a range of cutting edge high-throughput single cell molecular, spatial and cell phenotyping assays to map the structural and functional organization of the primate brain. We strive to build a catalytic brain cell reference and resource that will dramatically accelerate our understanding of brain structure, function and disease, and to create tools to help the community take advantage of these resources.

The Allen Institute will be generating several petabytes/year of spatial transcriptomics data to understand the fine scale distribution cell types in human and closely related non-human primate brains. This scientific data engineer position will contribute to the development of workflow and tools to register spatial transcriptomics to species matched reference brain template, deploying and maintaining pipelines for formatting, processing, and uploading spatial transcriptomics and related data to data archives and collaborator sites.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

Essential Functions
  • Work closely with scientists and engineers to develop computational and user workflows to register spatial transcriptomics data to species matched reference brain templates
  • Develop and maintain software tool to support co-analysis of registered images towards creation of multimodal common coordinate frameworks and atlases
  • Contribute to the deploying and maintaining pipelines for formatting, processing and uploading spatial transcriptomics and related data to data archives and collaborator sites
  • Develop code libraries, tutorials, and user guides to enable use and dissemination of the selected and/or developed registration and quality metric tools
Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management's assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience
  • Bachelor's degree in computer science, neuroscience, physics, mathematics, applied mathematics, engineering, or related field, or equivalent combination of degree and experience
  • Experience in scientific computing including Python and Linux/UNIX environment
  • Familiarity with modern software development best practices (e.g., git, GitHub)
Preferred Education and Experience
  • 0 - 2 years experience in scientific computing and analysis
  • Experience applying computer vision and image processing algorithms to imaging data
  • Experience in deploying simple user interfaces to enable manual input to and/or review output of image processing algorithms
  • Experience with scaling software from local to cluster/cloud-based use
  • Experience working in a shared code repository
  • Experience with cluster-based computing (e.g. Spark)
  • Experience with cloud-based computing (e.g. Amazon S3, Lambda, EMR)
Physical Demands
  • Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment
Position Type/Expected Hours of Work
  • This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.
  • Occasional travel to partner sites for collaborative development
  • Occasional attendance and participation in national and international conferences
Additional Eligibility Qualifications
  • In keeping with our focus on employee safety, all employees must be fully vaccinated against COVID-19 as a condition of employment unless a medical or religious exemption is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance and our policy.
Additional Comments
  • **Please note, this opportunity offersrelocation assistance**
Annualized Salary Range
  • $75,003 - $105,004 *
* Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable.

  • Employees (and their families) are eligible to enroll in benefits per eligibility rules outline in the Allen Institute's Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute's 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute's benefits offering are located at the following link to the Benefits Guide:

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.

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