Allen Institute for Brain Science

Software Engineer II – Data Science and Data Engin...

Job description

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 are seeking an exceptional, energetic and experienced Software Engineer who has a track record of building scalable and distributed production software solutions. The ideal candidate has experience in implementing data processing pipelines and data science models/algorithms to enable intelligent applications on top of petabytes of diverse data. We build workflows , frameworks, tools, and APIs to process, curate, analyze, organize and visualize large-scale neuroscience datasets. Our data and APIs are freely and openly shared with the public at .

The informatics solution will support the whole data science life cycle from ingestion, mapping, and refinement to publishing and serving, encompassing provenance of the data and integration across datasets, modalities, and scales from micro- to macro-scale and from raw data (sequences, images, videos, time-series) to derived models (cell types, circuits, brain organization). You will interact regularly with neuroscientists and collaborate closely with a wide variety of engineers in a large team while working on new discoveries about the brain.

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 as part of the informatics solutions development team to define the informatics architecture for the Allen Institute for Brain Science products and related activities
  • Work with subject matter experts to gather and analyze requirements and use cases and design architecture and modules capable of scaling out to meet anticipated growth
  • Create robust and efficient data pipelines to extract and transform data to quantitative features, knowledge, and visualizations to support new interactive modes of engagement with the data
  • Analyze current technologies, algorithms, models, and methods, and assess their fit for purpose
  • Implement rapid prototypes to flesh out and validate concepts
  • Responsibilities also include identifying, curating and transforming relevant datasets (e.g. , imaging data, video data, PostGres databases, CSVs)
  • Develop and maintain documentation to clarify requirements and rationale
  • Support internal and external teams as they integrate heterogenous unstructured, semi-structured and well-structured data into the data pipelines and master repository

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, Statistics, Mathematics, Physics, or other quantitative disciplines; or equivalent combination of degree and experience
  • 1 year of relevant experience in a team-oriented software development environment
  • Strong software development skills with proficiency in Python and SQL
  • Experience in operationalizing and optimizing software packages and systems, and data processing pipelines, analysis, algorithms, models in a production environment
  • Experience with scaling software from local to cluster/cloud-based use
  • Experience working in a shared code repository
  • Experience with cloud-based computing (e.g. Amazon S3, Lambda, EMR, etc.)

Preferred Education And Experience

  • Advanced degree in Computer Science, Statistics, Mathematics, Physics, computational neuroscience, or other quantitative disciplines
  • Command of best practices in software development life cycle
  • Experience with advanced algorithm and model design and implementation
  • Experience in deep learning (e.g., CNN) applied to image data a big plus
  • Experience building information systems that incorporate production databases
  • Familiarity with entire software toolchain, including source code management (git), build systems, debuggers, linkers, and profiling tools
  • Strong communication skills to concisely provide context, offer insights, and minimize misinterpretation
  • Experience in supporting data science algorithms and models in production such as monitoring, retraining, or editing for staleness and accuracy due to data changing, new data, assumptions etc.
  • Professional experience in C/C++ or Java a big plus
  • Experience with cluster-based computing (e.g. Spark)

Physical Demands

  • Fine motor movements in fingers/hands to operate computers and other office 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.

Additional Comments

  • **Please note, this opportunity does not offer relocation assistance**
  • **Please note, this opportunity offers work visa sponsorship**

Annualized Salary Range

  • $105,196 - $147,274 *
  • 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 outlined 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 Institute's 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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