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Software Engineer II - Contracted Position

Department: 4000- IT
Location: Seattle

Software Engineer II – Large Scale Data Sets

The Allen Institute for Brain Science seeks a Software Engineer II (SWE) to develop standards and tools to support the sharing of large-scale neurophysiology data. The Neurodata Without Borders (NWB) project aims to create standardization for neurophysiology data and related metadata to enable broad reproduction, interchange, and reuse.

The project has already produced and released a first version of the NWB standard and is now working on the second major version. This highly collaborative position will require the SWE to be the primary developer to extend the NWB format to support a variety of experiments from multiple institutions.

The ideal candidate will have experience processing and analyzing rodent neurophysiology or related data, a solid understanding of data modeling and schema development, and a proven track record of on-time delivery of technology products.

Job Responsibilitie

  •  Working knowledge of a variety of semantic modeling techniques; ability to evaluate tradeoffs between formality and usability; ability to decide when to borrow from an existing ontology and when to develop new structures
  • Collaborate with scientists and technologists to architect and implement an NWB schema extension that supports:

o   the representation of rodent brain anatomy and coordinate systems

o   the use of genetic tools to target specific cell populations

o   representation of behavioral tasks and sensory stimuli through analysis of identified use cases of experiments from multiple institutions

  • Analyze data relationships and content, develop new semantic representations, and work with subject matter experts and end users to inform the development and modeling of new semantic representations to improve data accessibility and reuse
  • Collaborate with the NWB developer community to integrate the schema extension into NWB API libraries
  • Identify and build working relationships and partnerships with external collaborators, data providers, and semantic technology users
  • Participate in championing, communicating, and maintaining internal and external (collaborative) efforts in data integration and standardization, for example through hackathons and workshops
  •  Develop controlled vocabularies and apply metadata
  • Participate in writing, presenting, and reviewing strategic and operational reports
  • Apply a modern software engineering workflow, including emphasis on code review, continuous integration, and automatic testing


  • Bachelor’s in Computer Science, Mathematics, Bioinformatics or related field
  • 5+ years of experience with data management systems and/or integration of big data from multiple sources
  • Extensive coding experience in Python as part of a software product
  • Experience developing and supporting a team
  • Experience driving and delivering on independent projects
  • Proven written and oral communication skills


  • Advanced degree in Computer Science, Mathematics, Bioinformatics or related field
  • Experience with applied ontology development (RDF(S)/OWL, SPARQL, the Semantic Web or Frame based KR systems)
  • Domain knowledge in rodent neurophysiology data acquisition, and analysis
  • Understanding of taxonomy design best practices and experience implementing large-scale taxonomy and/or ontology projects with a user-centered focus
  • Excellent organizational management skills and a sense of diplomacy
  • Enthusiasm for working closely with cross-functional colleagues and stakeholders


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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