Career Opportunities with Allen Institute for Brain Science

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Software Engineer II/III – Informatics Development (Limited-Term)

Department: 4000 - Data and Technology
Location: Seattle

Software Engineer II/III – Informatics Development (Limited-Term)

Our mission at the Allen Institute for Brain Science is to accelerate the understanding of how the human brain works in health and disease. Using a team science approach, we strive to drive technological innovations and discover fundamental brain properties through the integration of experiments and simulation. We generate large-scale neuroscience datasets, online search, visualization, and analysis utilities, and APIs. Our data is freely and openly shared with the public at

The Allen Institute for Brain Science seeks a Software Engineer II/III (SWE) for a limited term (for the remainder of 2020) to join the informatics solutions development team. This SWE will be responsible for managing large scientific data sets and analysis pipelines serving neuroscience and brain imaging research communities around the world.

This highly collaborative position will require the SWE to be the primary developer on multiple data analysis software packages used for high-throughput analysis and modeling of physiology activities in the mouse cortex in response to sensory stimuli and while performing behavioral tasks.

The SWE will collaborate with data production teams to design high-throughput data collection and analysis workflows, ensure that their software can be built and deployed in multiple research laboratories around the world, and facilitate standardized data generation and analysis in the community.

Our team uses popular and modern software tools in our Linux-based workflow. Most analysis code will be implemented in Python, although other languages could be required. Your code runs independently, but it will also be integrated into our custom laboratory information management system, which is written in Ruby on Rails, running on PostgreSQL.

To gain more insight on the projects you will impact, please visit the Allen Institute Brain Observatory website: link to:

Essential Duties

  • With scientific analysis teams, design files, metrics and visualizations representing neural activity.
  • Monitor ongoing data quality and analysis results as part of curation for regular public data releases.
  • Use software engineering principles to write, maintain, and deploy robust scientific software based on high level functional requirements and team input.
  • Externalize this work in an SDK and document it well so that others can leverage your contributions.
  • Collaborate effectively with experts in diverse scientific and engineering topics, including neuroscience, high performance scientific computing, machine learning, and computer vision, and web applications.
  • Apply a modern software engineering workflow, including emphasis on software design, code review, continuous integration, and automatic testing.
  • Create simple dashboards to visualize and summarize experimental data for review and validation.

Required Education and Experience

  • Bachelor’s degree in a relevant technical discipline.
    • SWE II: 3-5 years of relevant experience in a team-oriented software development environment.
    • SWE III: 6 + years of relevant experience in a team-orientated software development environment.


  • Expert level development experience in at least one general purpose, dynamically typed object-oriented language (e.g., Python).
  • Expert level experience in scientific computing software (Python, MATLAB).
  • Demonstrated experience in data analysis, preferably in signal processing and numerical methods.
  • Proficient in SQL and database design.
  • Experience with command line development tools in a Linux environment.
  • Familiarity with entire software toolchain, including source code management (git), debuggers, and testing methodologies.
  • Experience writing code and configuring systems to facilitate automated testing, building, and deployment of software.
  • Ability to gather requirements from collaborators, synthesize into development work items, describe to colleagues and discuss implementation ideas, record issues, execute and complete.
  • Ability to define stopping points and close issues.

Preferred Education and Experience

  • Advanced degree in a relevant technical discipline.
  • History of contributing to open source projects.
  • Experience writing code for continuous delivery, especially using Bamboo Continuous Integration and Build Server.
  • Interest in neuroscience and curiosity about how the brain works.
  • Experience with NWB (Neurodata Without Borders).
  • Experience working on an Agile development team.

Additional Eligibility Qualifications

  • COVID-19 Remote Work Flexibility will be discussed with candidates as part of the interview cycle.

**Please note, this opportunity does not sponsor work visas and has no 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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