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Software Engineer I - Neuroscience Modeling

Department: Modeling and Theory

Software Engineer – Modeling Software for the Neuroscience Community – MindScope

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 MindScope program seeks to understand the transformations, sometimes called computations, in coding and decoding that lead from photons to behavior and conscious experience by observing, perturbing, and modeling the physical transformations of signals in the cortical-thalamic visual system within a few perception-action cycles.

We are seeking a Software Engineer to join the BRAIN Initiative-sponsored project dedicated to disseminating modeling tools and supporting users of these tools in the neuroscience community.

The engineer will develop software and help support existing open-source tools like the modeling suite BMTK (, modeling data format SONATA (, and the visualization package VND (

These freely available tools facilitate scientific projects involving computational modeling and simulations of brain cells and networks. They are used by a growing number of scientists in the community, and our aim is to support these users and continue improving the tools to meet their needs.

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

  • Support users of our modeling tools by implementing user-requested features, fixing bugs, and resolving issues and questions submitted to the team
  • Support dissemination of our tools by maintaining documentation, providing diverse venues for downloading and installing the software, including on the cloud, and participating in tutorials, training, and workshops aimed at educating users
  • Conduct outreach activities such as interviews and surveys of users

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

  • Bachelors degree in Computer Science, Computational Neuroscience, and related fields, or equivalent combination of degree and experience
  • Experience with scientific and visualization Python stack, or experience in similar languages like Matlab, R, Julia
  • Familiarity with modern version control systems, such as git
  • Experience with software design, development, and maintenance
  • Experience with Linux

Preferred Education and Experience

  • Strong background in scientific computing
  • Experience in developing scientific modeling software, especially in computational neuroscience
  • Experience with parallel computing

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 remotely due to COVID-19 and our focus on employee safety. We are a Washington State employer, and remote work must be performed in Washington State. We continue to evaluate the safest options for our employees. As restrictions are lifted in relation to COVID-19, this role will return to work onsite.

Additional Comments

  • **Please note, this opportunity does not sponsor work visas **
  • **Please note, this opportunity may offer 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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