Summer Intern – Neural Dynamics / Big-Data Imaging Libraries in Cloud Environments

Summer Intern – Neural Dynamics / Big-Data Imaging Libraries in Cloud Environments

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 Neural Dynamics is to answer fundamental questions about brain function. Specifically, how does our brain build our understanding of the complex world around us to guide the flexible behaviors that address our biological needs? The answers will be in terms of defined neuron types interacting across the whole brain and body, requiring us to develop next-generation neurotechnologies and employ a team-based approach for discovery neuroscience. Knowledge, data, and tools will be widely shared, in part to support the development of therapies for brain disorders.

We are seeking a summer intern to join the Scientific Computing department for the summer of 2023. They will work on improving big-data imaging tools in cloud environments.

There is a plethora of imaging data being collected, and there are many graphical libraries available to interact with this data. These include DeepLabCut (an ML package that can learn how to label the anatomical features of mice in video recordings), napari (a fast, multi-dimensional image viewer in Python that can be used for neuroscience imaging), and ImageJ (similar to napari but Java based). Traditionally, these packages were installed and used on local desktops. However, with the rising trend of cloud computing, most of the datasets are being hosted online. It is becoming increasingly cumbersome and expensive to download data locally, and so a cloud computing solution is required. We need to stand-up desktop virtual machines hosted in our cloud computing environments that scientists can log into and use their favorite imaging libraries without the need of downloading large datasets. The goals of this internship are to write the scripts that will spin up these virtual environments on the cloud and to have hands-on experience learning best software practices.

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.

Educational Objectives

• Hands-on experience with Infrastructure-as-Configuration (e.g. Terraform, CloudFormation)
• Learn more about the imaging libraries neuroscientists use in their workflow (napari, ImageJ, DeepLabCut, etc.)
• Learn how to use Identity and Access Management tools to manage permissions for cloud users
• Learn how to optimize the interactions of storage and computing processes

Applicant Requirements

• Currently enrolled in, or a 2023 graduate of an accredited associate, bachelor’s, or master’s program
• Must be able to start on either June 5^th or June 20^th, 2023 and commit to the full 10-week internship
• Must be eligible to work in the United States for the duration of the internship
• Must be 18 years of age or older

Work Environment

• Desk job in typical office environment

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment

Position Type/Expected Hours of Work

• This is a limited term position for no more than 10 weeks
• Expected work schedule is 35 – 40 hours a week over this period, M-F
• 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

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

Additional Comments

• **Please note, this opportunity does not sponsor work visas**
• **Travel and/or housing stipend available to qualifying interns**

Compensation

• $18.69 per hour plus relocation and/or housing support.

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.