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Engineer II, Modeling and Theory

Department: Modeling

Engineer II, Modeling and Theory

The mission of the Allen Institute for Cell Science is to create multi-scale visual models of cell organization, dynamics, and activities. Our approach encompasses large scale data collection, observation, theory, and predictions to understand cellular behavior in normal and pathological contexts. As a division within the Allen Institute, the Allen Institute for Cell Science uses a team-oriented approach, focusing on accelerating foundational research, developing standards and models, and cultivating new ideas to make a transformational impact on science.

The Allen Institute for Cell Science uses 3D live cell imaging to generate unprecedented data for the analysis of the cell and its components as an integrated system. We seek a talented engineer to join the Computational Biology and Machine Learning Team to help build, analyze, and deploy sophisticated computational models of cell states and dynamic cellular processes that leverage these rich images and movies independently and in concert with diverse complementary data. Research at the Institute is highly collaborative, requiring scientists and engineers to work across disciplines, focusing on high impact biological questions and establishing/maintaining the highest standards for best practices and computational rigor.

The role of this position is to implement and deploy (on-premises and in the cloud) large-scale analysis workflows that include deep learning components and that combine live cell microscopy image data with transcriptomic and other Institute-generated data in order to study cellular organization and cellular state transitions. Examples of relevant current projects are here and here.

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.

**Applicants should include a brief cover letter (max 1 Page) explaining why they are a good fit for this position.**

Essential Functions

  • Collaboratively develop and apply computational analyses to describe intracellular organization using live cell microscopy image data in a variety of Institute projects
  • Participate in bringing large-scale data analysis workflows to operate in a cloud environment
  • Promote integration and sharing of tools, resources, models, and data across the Institute
  • Work across teams to transform prototype models into professionally packaged and reusable applications with intuitive and accessible visualizations

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects managementís assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience

  • Bachelorís Degree in computational biology, bioinformatics, machine learning, statistics, applied mathematics, computer science/electrical engineering, or related field
  • Minimum 1 year of experience with high dimensional statistical techniques and modeling approaches in biology applications
  • Experience with cloud-computing
  • Demonstrated proficiency in scientific computing including Python and Linux/UNIX environment

Preferred Education and Experience

  • Masterís degree in computational biology, bioinformatics, machine learning, statistics, applied mathematics, computer science/electrical engineering, or related field; or equivalent combination of degree and experience
  • Experience working with biological image data and/or large publicly available biological image data resources, such as the Human Protein Atlas
  • Experience utilizing software engineering practices such as version management, build management and testing
  • Desire to learn about scientific projects and to develop creative solutions for problem solving and standardization
  • Creation or contribution to sharable open-source scientific codebase
  • Strong communication skills and ability to work in a collaborative, multi-disciplinary environment

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 offers relocation assistance**
  • **Please note, this opportunity sponsors work visas**

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. We offer competitive pay, generous benefits, and a dynamic work environment. The Allen Institute for Cell Science is an equal opportunity employer





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