Scientific Data Engineer I - Bioinformatic and Machine Learning

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 seek a scientific data engineer experienced with modern applied statistics and machine learning to model multimodal neuroscientific data collected on cutting-edge data generation platforms. This position is situated within the imaging department which consists of ~20 scientist and research associates using widefield, confocal, 2-photon, and light-sheet microscopes. You will collaborate with an enthusiastic, dynamic and growing team (~10) of computational and experimental scientists within the imaging department to build an infrastructure for the large-scale analysis of spatial transcriptomics data. Potential projects include: 1) Develop an automated pipeline for quality control of spatial transcriptomics data. 2) Integration this data with other modalities using machine learning approaches to generate multimodal atlases of brain tissue. 3) Establish visualization platforms to share the data with internal and external collaborators. This infrastructure will be of crucial importance to future atlasing projects, which include a developing mouse brain atlas as well as human and non-human primates brain atlases. The work will be part of multiple larger project that have long-term funding through the Brain Initiative Cell Atlasing Network (BICAN). The ideal candidate will have experience building computational models from large-scale datasets and engage collaboratively with data collection and data engineering teams to ensure model efficacy.

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

• Conceive, develop, and implement statistical and machine learning models to drive discovery from large biological datasets
• Participate in a highly interactive and multidisciplinary environment
• Influence data collection and processing pipelines to improve data quality and model performance
• Effectively communicate findings across the institute as well as to the greater scientific community in peer-reviewed journals, scientific conferences, and web documentation
• Practice software development best practices and follow industry standards

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

• Bachelor’s degree in computer science, neuroscience, physics, mathematics, applied mathematics, engineering, or related field, or equivalent combination of degree and experience
• Experience in applied statistics and machine learning
• Command of current statistics and machine learning literature
• Experience in scientific computing including Python and Linux/UNIX environment

Preferred Education and Experience

• 0 – 2 years of equivalent experience
• Demonstrated success working on interdisciplinary projects
• Experience in high-performance scientific computing
• Experience in computational neuroscience
• Familiarity with best practices for open-source software development
• Familiarity with NGS analysis packages

Physical Demands

• Fine motor movements in fingers/hands to operate computers and lab equipment

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.

Travel

• Attendance and participation in national and international conferences required (travel may not be required to attend)

Additional Eligibility Qualifications

• In keeping with our focus on employee safety, all employees must be fully vaccinated against COVID-19 as a condition of employment unless a medical or religious exemption is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance and our policy.

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity offers work visa sponsorship**

Annualized Salary Range

• $75,003 - $105,004 *

• Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable.

Benefits

• Employees (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 Institute’s 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.