Senior Cloud Platform Engineer
About The Position
We are seeking a Senior Cloud Platform Engineer to join our Bioinformatics and Cloud Platform team. This is a highly hands-on role focused on operating, improving, and scaling the scientific computing infrastructure that powers production bioinformatics workflows. You will work at the intersection of bioinformatics, cloud infrastructure, and platform engineering, helping scientists run complex next-generation sequencing (NGS) workflows reliably and at scale in AWS. You will ramp up on our platform while actively contributing to its operation and improvement. As you gain familiarity, you will take on increasingly complex challenges — including solution architecting to support new bioinformatics workflows and enhancing platform capabilities. This role spans multiple layers of the platform, from infrastructure to bioinformatics workflows, and is well-suited for engineers who enjoy working across system boundaries. You’ll collaborate closely with scientists and engineers, contributing wherever needed to keep the platform running smoothly and evolving. Over time, you will develop deep expertise in the platform, take ownership of key infrastructure components, and help shape the long-term architecture of our scientific computing environment.
Requirements
- MS in Science, Engineering, Bioinformatics, Computational Biology, or related field
- 4+ years of experience working in pharma, biotech, or life sciences
Nice To Haves
- Hands-on experience working with NGS and bioinformatics workflows languages (Nextflow, Snakemake)
- Strong Linux systems expertise
- Strong AWS experience, including IAM, EC2, S3, networking fundamentals
- Experience integrating systems across cloud and enterprise environments
- Demonstrated ability to debug complex systems spanning multiple technologies
- Ability to work independently and take ownership of problems
- Demonstrated ability to learn new technologies quickly and work across unfamiliar systems
- Experience with orchestrating and scaling scientific or data workflows in cloud or on-prem environments
- Experience with infrastructure as code or automation tools to manage compute, storage, and networking resources
- Familiarity with data engineering, distributed compute, or high-throughput analysis platforms
- Experience supporting collaborative data science or research environments
- Exposure to CI/CD pipelines and modern DevOps practices (Jenkins, GitHub Actions)
- Experience developing or implementing testing frameworks for pipelines, workflows, or infrastructure
- Experience integrating with enterprise platforms, internal tools, or regulated systems
- Comfortable learning new tools and platforms quickly, adapting to changing environments, and working across multiple technologies
Responsibilities
- Operate and improve our cloud platform that runs production NGS and bioinformatics workflows
- Support and troubleshoot scientific workflow pipelines (Nextflow preferred)
- Operate and debug Linux-based production environments
- Investigate and resolve complex issues across the entire platform stack, including workflow orchestration, cloud compute and storage, networking and security, IAM, and application services
- Partner with scientists to translate workflow needs into scalable, secure platform solutions
- Contribute to infrastructure automation and platform reliability improvements
- Integrate and operate multiple research and enterprise platforms
- Apply cloud security and operational best practices
- Participate in technical roadmap discussions and platform architecture decisions
Benefits
- Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).
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What This Job Offers
Job Type
Full-time
Career Level
Senior
Number of Employees
5,001-10,000 employees
