Lead Bioinformatician/Engineer – Pipelines, Infrastructure

This is a fully remote position, open to applicants in United States.

📋 Description

• Take charge of pipeline and infrastructure engineering for a research informatics team focused on cell-free DNA screening in Women's and Organ Health.

• Enhance and maintain WDL workflows utilizing AWS Batch and AWS HealthOmics.

• Oversee the execution of new Nextflow workflows and existing WDL workflows on shared tools and infrastructure.

• Simplify the pipeline process for scientists to run effectively without needing engineering assistance.

• Manage the team's AWS infrastructure, utilizing Terraform for infrastructure as code.

• Enhance reliability, reproducibility, and observability within compute environments.

• Develop testing, monitoring, and alerting systems to identify failures proactively before scientists encounter them.

• Strengthen internal tools to minimize manual tasks and aid in production issue resolution.

• Facilitate easier testing, documentation, and transition of new capabilities.

• Utilize coding agents for implementation, code reviews, investigations, and operational triage while reviewing and testing all resulting code.

• Collaborate with science leads and data scientists to integrate new methods into production pipelines and assess their modifications.

• Work alongside the production organization to ensure readiness for capabilities transitioning out of research.

• Independently manage the team's pipelines and infrastructure without oversight.

• Transition new workflows onto shared tools and infrastructure.

• Empower scientists to run and troubleshoot their own pipeline work.

• Minimize operational disruptions to scientific activities.

⛳️ Requirements

• Bachelor's degree in Bioinformatics, Computer Science, Computational Biology, or a related discipline; however, equivalent experience is also considered.

• At least 4 years of experience in software or pipeline engineering, ideally within life sciences, sequencing, or a production-adjacent environment.

• Proven track record of end-to-end ownership of a system operated in a production setting.

• Strong background in Python and software engineering principles, including testing and debugging skills.

• Familiarity with at least one workflow system such as Snakemake, CWL, WDL, Nextflow, or a similar platform.

• Practical experience with cloud computing, preferably AWS, including infrastructure as code; experience with Terraform is preferred, but other tools are acceptable.

• Solid understanding of Linux, containerization, and version control practices.

• Developed at least one AI-assisted workflow currently in use, with the ability to articulate what it replaced and how its effectiveness is measured.

• Proven ability to quickly learn and adapt to unfamiliar tools.

• Strong written communication skills and ability to create actionable documentation.

• Direct experience with WDL or Nextflow may be advantageous.

• Familiarity with AWS Batch or HealthOmics could be beneficial.

• A scientific curiosity to comprehend the biology underlying the pipeline and pose insightful questions may be advantageous.

🏝️ Benefits

• Comprehensive medical, dental, vision, life, and disability insurance plans for eligible employees and their dependents.

• Complimentary testing for employees and their immediate families.

• Fertility care support.

• Leave policies for pregnancy and bonding with a newborn.

• 401k retirement plan benefits.

• Commuter benefits.

• Generous employee referral program.