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Scientific Data Engineer II – Computational Neuroanatomy (Data & Technology) Brain Science

Department: Data and Technology

Scientific Data Engineer II – Computational Neuroanatomy (Data & Technology) Brain Science

The mission of the Allen Institute 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 Allen Institute 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.

We seek to hire an exceptional software engineer to create an extensible brain knowledge base and toolsets spanning multiple species, modalities and developmental stages. The position will work with interdisciplinary teams to harmonize and aggregate cell and anatomical data through several keys’ dimensions of evolutionary and developmental trajectories, anatomy and common coordinate frameworks, cell features and taxonomies and the meta-dimension of claims and evidence that supports reuse and reproducibility. This framework will allow unprecedented data and knowledge exploration to empower cell type neuroscience research and be flexible enough to integrate related research outcomes.

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

  • Access, convert and curate neuroscience data and analysis from many different formats and sources for integration into the knowledge base
  • Collaborate with interdisciplinary teams to select, use, and extend data models and ontologies
  • Develop expert-guided and data-driven 3D anatomical models across the whole mouse brain and during development and disease trajectories
  • Develop a code library, tutorials, and user guides to enable the use and understanding of knowledge base data models and harmonized by analysis and visualization pipelines
  • Develop or apply algorithmic tools to support image and data analysis
  • Develop prototype applications demonstrating the use of the knowledge base in analysis and visualization
  • Interface with and support community use of the knowledge base in external analysis and visualization applications
  • Participate in a highly interactive and multidisciplinary environment
  • Write and publish manuscripts, grant and internal progress reports and grant applications
  • Present findings in peer-reviewed journals and scientific conferences

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 Neuroscience, Computational Neuroscience, Bioinformatics, Genetics, Physics, Applied Mathematics, Engineering, Computational Biology, Computer Science or related field; or equivalent combination of degree and experience
  • 1 or more years of experience in computational data analysis

Preferred Education and Experience

  • Expert level experience in 3D data graphics and visualization
  • Experience in scientific computing including Python and Linux/UNIX environment
  • Experience in scientific data applications
  • Knowledgeable about neuroanatomy and brain architecture
  • Positive attitude, self-motivated, and ability to troubleshoot
  • Exceptional oral and written communication skills
  • Ability to work independently and within a collaborative, multi-disciplinary environment to meet aggressive timelines

Work Environment

  • Working at a desk in an office setting

Physical Demands

  • Occasional lifting up to 30 pounds
  • 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 position is funded through grants awarded by the NIA and NIH
  • 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.


  • Attendance and participation in national and international conferences required

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 offers relocation assistance**

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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