Software Engineer II – Read Team - Seattle Hub for Synthetic Biology

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 Allen Institute, in partnership with the Chan Zuckerberg Initiative and the University of Washington, recently launched the Seattle Hub for Synthetic Biology (SeaHub), a new initiative at the intersection of academic creativity and start-up-style execution. The SeaHub mission is to generate the foundational datasets, models, and molecular infrastructure to reengineer cells to record their own histories and reprogram disease to health. Take off with us as we imagine — and create — a kind of cellular flight recorder that can also seize the controls.

SeaHub is looking for an imaginative software engineer to help us to record information in the genomes of cells and recover that information through various next-generation sequencing-based methods, including single-cell RNA sequencing. The software engineer’s primary responsibility will be to create and maintain computational pipelines to reproducibly process and analyze sequencing data. These pipelines will operate on terabyte-scale short read (Illumina) and long read (PacBio, ONT) datasets, and will use AWS to enable scale and rapid deployment. The software engineer will also advise us in the creation of new biological programming languages from building blocks like DNA Typewriter, ENGRAM, and P3 (see references below).

For this role, we need a software infrastructure enthusiast who is also excited by the potential to create nucleic acid-based languages to process and store diverse biological signals, as well as incorporate logic functions, error-correction, and other ideas from non-biological systems. The software engineer will be a member of the computational biology (“Read”) team and will also need to collaborate extensively with our experimental biology teams (“Sense”, “Write”, “Build”).

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

• Assist in the development and maintenance of NGS/bioinformatic/computational biology pipelines
• Develop documentation for data workflows, software, and processes
• Create and manage Amazon Web Services (AWS) Amazon Machine Images (AMIs)
• Optimize storage infrastructure for cost, performance, and redundancy
• Develop solutions for synchronizing data between on-premises instruments and AWS storage
• Partner with computational biologists to deliver development & operational solutions for data organization, interrogation, and presentation

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 Engineering, Computer Science, Bioinformatics, or related discipline; or equivalent combination of degree and experience
• One (1) year relevant experience

Preferred Qualifications

• 2-4 years of equivalent experience
• Scientific interest or experience in genome engineering, genomic recording, genome editing, and genomics/sequencing
• Aptitude in one or more programming languages, e.g., R, C , and/or Python (Python preferred)
• Fluency in cloud computing, Snakemake, and Nextflow
• Strong working knowledge of high-performance computing infrastructure and concepts
• Experience with version control, writing code, common code bottlenecks and solutions, and configuring systems to facilitate automated testing, building, and deployment of software
• Ability to work in and fast and dynamic environment
• Passion for building databases, pipelines, and other infrastructure to support NGS / bioinformatics analysis
• Experience with NGS datasets
• Experience writing code for continuous delivery
• Experience with container technologies such as Docker or Apptainer
• Fluency in machine learning and artificial intelligence
• Advanced degree in a relevant technical discipline (e.g., computer science, bioinformatics, or genomics)
• History of contributing to open source and/or team-based projects
• Outstanding communication and presentation skills
• Strong project management and organizational skills

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 working onsite and is expected to work onsite for 80% of working hours. We are a Washington State employer, and the primary work location for Allen Institute employees is 700 Dexter Ave N.; any remote work must be performed in Washington State

Travel

• The successful applicant may be invited to attend occasional national and international conferences

Academic References

• DNA Typewriter: https://www.nature.com/articles/s41586-022-04922-8
• ENGRAM: https://www.biorxiv.org/content/10.1101/2021.11.05.467434v1
• P3: https://www.biorxiv.org/content/10.1101/2023.08.14.553235v1
• SeaHub: https://alleninstitute.org/division/seattle-hub-for-synthetic-biology/

Additional Comments

• Please provide a cover letter with your application

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

Annualized Salary Range

• $108,350 - $151,650 *

* Final salary depends on the required education for the role, experience, level of skills relevant to the role, and 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 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.