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Sr. Software Engineer - Bioinformatics

Department: 4000 - Data and Technology
Location: Seattle

Sr. Software Engineer - Bioinformatics 

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Our Brain Science team is dedicated to accelerating 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 energetic and experienced software engineer who has a track record of building robust and scalable production software. The ideal candidate has experience in implementing data architecture and pipelines to enable the production, analysis, and exploration of large-scale single cell transcriptomics data.

The position is created to support the whole data life cycle from ingestion, mapping, refinement to publishing and serving. Support encompassing provenance of the data, itís integration across datasets from raw data (sequences) to derived models (cell types, circuits, brain organization). You will be working with subject matter experts and development teams to gather requirements, assess different methods for fit for purpose, implement rapid prototypes to flush and validate concepts and contribute to the implementation of production solutions. This role is part of an organization doing big and open science. You will interact regularly with neuroscientists and a wide variety of engineers, collaborating in a large team working on new discoveries about the brain.

Essential Duties

  • Work with development teams to clarify requirements and rationale.
  • Develop and maintain documentation for data workflows, software and processes.
  • Spearhead design of robust and efficient data pipelines to extract and transform data from sample processing, sequencing, data processing and to generation of quantitative features.
  • Monitor ongoing data integrity and analysis results, working with data generation and product teams to efficiently process the data to meet internal and external user needs.
  • Collaborate effectively with experts in diverse scientific and engineering topics, including neuroscience, high performance scientific computing, computer vision, and web applications.
  • Exemplify a modern software engineering workflow, including emphasis on code review, continuous integration, and automatic testing.

Required Experience and Education

  • Bachelor's degree in Statistics, Computer Science, Physics or related field
  • 6 + years experience in a related field 
  • Experience with large datasets such as single cell transcriptomics or genomics
  • Experience with advanced methods in generating and analyzing scientific data
  • Strong software development skills, with proficiency in Python and C++ preferred
  • Deep understanding of software development life cycle
  • Experience building information systems that incorporate production databases
  • Working experience in a cloud environment

Preferred Experience and Education

  • Experience with research in biological sciences
  • Advanced degree in Statistics, Computer Science, Physics, or related field
  • Familiarity with entire software toolchain, including source code management (git), build systems, debuggers, linkers, and profiling tools
  • Exceptional problem-solving abilities will be essential for success
  • Strong communication skills to concisely communicate to provide context, offers insights and minimizes misinterpretation

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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