Postbaccalaureate Research Assistant – Brain Science / Improving interoperability of patch-seq data through ontology mapping and GenAI tools

Postbaccalaureate Research Assistant – Brain Science / Improving interoperability of patch-seq data through ontology mapping and GenAI tools

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 mission of the Allen Institute for Brain Science is to accelerate 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 a Postbaccalaureate Research Assistant to support integration of a multimodal experimental technique, "Patch-Seq", for improved data interoperability. Patch-Seq is a powerful technique that links the transcriptomic profile of individual neurons to their morphology and electrophysiological properties, offering a unique opportunity to bridge historic and modern classifications of brain cell types. In this role, you will work closely with leading scientists, bioinformaticians, and engineers to develop data dictionaries, align experimental terminology with community-standard ontologies, and test AI-driven tools for term mapping and annotation. Your efforts will help advance open science by creating reusable workflows and machine-readable data models that ensure consistency and interoperability across the global neuroscience community.

This position provides a rare opportunity to contribute to high-impact, internationally recognized research in data standards and life science data integration. You will gain expertise in data standardization, open data principles, and the application of AI tools for metadata alignment and data annotation. Over the course of the project, you will become proficient in developing technical frameworks, schemas, and ontologies while collaborating with national data archives, research consortia, and specialized institutes. By the end of the program, you will have made a meaningful contribution to data-sharing best practices and gained valuable experience in software tools and data management, positioning you for future success in neuroscience, bioinformatics, or data science.

In the first month, the candidate will become oriented with our tools, the nature of the data, and community standards. In the next month, the candidate will develop an initial data dictionary for one aspect of patch-seq data and begin testing GenAI tools for term mapping to common data elements and provide feedback to the tool generators. The remainder of the time will involve developing a workflow using GenAI tools and to compile a repository of their Common Data Elements describing patch-seq experimental metadata and data metrics.

This role is a unique opportunity for those with an undergraduate background to make a significant contribution to high impact, internationally recognized research projects that are at the forefront of defining best practices in data standards and management for modern life science research. You will gain an understanding of the principles of open data and data sharing as well as data standardization and the tools relevant to these practices during this postbaccalaureate program. You will also gain experience and expertise in software designed to facilitate such work and contribute to the projects, consortia, working groups, and publications related to this data integration.

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.

Applications must be received by January 7, 2025, to be considered.

Educational Objectives

• Learn about controlled transformation of scientific data through standardized pipelines to facilitate knowledge integration and open sharing and reuse
• Discover the power of ontologies for interoperability by contributing to the creation of common scientific language to connect diverse datasets for easier discovery and analysis
• Learn about best practices in metadata development and usage for annotation of datasets for search and visualization, including contributions to a compendium of cell types
• Dive into data modeling with modern tools like LinkML and Polars and participate in creating models that facilitate seamless integration across scientific domains
• Gain experience managing data for cutting-edge sequencing technologies
• Develop problem-solving skills in a complex, collaborative research environment to address challenges in research data integration
• Experience a software engineering environment and learn technology project management tools and processes (Confluence, Jira, Agile, GitHub, AWS)
• Learn to collaborate with workers on teams with diverse roles, including research scientists, bioinformaticians, web app developers, IT infrastructure engineers, project, and product managers
• Gain experience with data curation and testing for generative AI tools used in vocabulary management
• Learn to collaborate with workers on teams with diverse roles, including research scientists, bioinformaticians, web app developers, IT infrastructure engineers, project, and product managers

Required Education and Experience

• Bachelor’s degree
• Demonstrated commitment to science

Work Environment

• Data Center

Position Type/Expected Hours of Work

• This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.

Additional Eligibility Qualifications

• Completed a bachelor’s degree (or will have completed by the start of the program) and does not have an advanced degree in the role’s relevant STEM field
• Must be able to start in June or July 2025 and commit to the full one-year program, which will end on Friday, May 29, 2026
• Must be eligible to work in the U.S. for the program duration
• Must be 18 years of age or older

Additional Comments

• Postbacs are expected to participate as fully-engaged team members, attending and participating in team meetings, presenting on their work, etc.
• Aside from program activities, postbacs are expected to work full-time as regular team members unless otherwise approved by their manager
• **Please note, this opportunity offers relocation and housing assistance**
• **Please note, this opportunity requires U.S work authorization and does not sponsor work visas**

Annualized Salary

• $59,280 (non-negotiable)

Benefits

• Postbacs (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

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.