Director - Cloud Platforms & Agent Infrastructure

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world.
Location: San Diego, CA; San Francisco, CA; Louisville, CO; Indianapolis, IN; Boston, MA
Reports to: Head of Architecture4Insight, Data Foundry
Overview
At Lilly, we serve an extraordinary purpose. We make a difference for people around the globe by discovering, developing and delivering medicines that help them live longer, healthier, more active lives. Not only do we deliver breakthrough medications, but you also can count on us to develop creative solutions to support communities through philanthropy and volunteerism.
Lilly Small Molecule Discovery is an organization purpose-built to create molecules that make life better for people. We focus on using cutting edge science to unlock new approaches that can treat people suffering from diseases with poor treatment options. We continually challenge ourselves to deliver molecules that can provide breakthrough efficacy with the highest possible safety margins. We are dedicated to optimizing our mindset, technology, and processes for faster, more nimble execution. Our success is built on a culture that empowers innovative problem solving through open collaboration and individual accountability.
Discovery Technology and Platforms is a newly established function within this organization. Its mission is to accelerate molecule discovery by building highly optimized foundational platforms, streamlining lab operations through advanced technologies and data connectivity, and intentionally investing in novel technologies and capabilities.
About Data Foundry
Data Foundry is a multidisciplinary team dedicated to enabling and accelerating molecule discovery through scalable and reproducible data generation, fueled by advanced scientific computing, informatics, and automation solutions. Data Foundry operates through four integrated pillars: Architecture4Insight (data infrastructure and scientific software), Methods4Insight (analytical and computational methods), Scale4Insight (lab automation and agentic workflows), and Preparedness4Insight (data governance and readiness). Together, these pillars empower every Lilly scientist to make optimal decisions by providing seamless access to data, insights, and AI-driven capabilities at scale.
Position Summary
The Senior Director, Cloud Platforms & Agent Infrastructure will lead technical architecture and platform engineering for Data Foundry's cloud-native infrastructure. Reporting to the Head of Architecture4Insight, you will build scalable, secure, and agent-ready systems that enable both human scientists and autonomous AI agents to accelerate molecule discovery.
You will architect and operate the computational infrastructure, APIs, and workflow automation systems that power real-time data access, analytical method deployment, and agent-driven experimentation — partnering closely with the Frontier AI group to ensure autonomous agents can reliably access data, invoke methods, and control laboratory systems at scale. As the enabling foundation across all Data Foundry pillars, this role provides Methods4Insight with production-ready platforms for deploying analytical methods as agent-callable APIs; integrates with Automation & Scale4Insight for real-time data capture from laboratory instruments; and partners with Preparedness4Insight to embed governance, metadata standards, and FAIR principles directly into platform design.
The ideal candidate brings proven experience building cloud-native platforms in life sciences, deep expertise in modern software architecture and DevOps, and a track record of translating scientific requirements into scalable technical solutions. Experience with AI agent workflows or MCP server infrastructure is highly valued.
Responsibilities

Lead the design and operation of Data Foundry’s cloud-native infrastructure (AWS, Azure, and/or GCP), including infrastructure-as-code, containerization, orchestration, and self-service platforms that empower discovery scientists to deploy tools and run analyses at scale.
Partner closely with the Frontier AI group to build agent-ready infrastructure—including APIs with structured error handling, versioning, and audit trails; Model Context Protocol (MCP) servers; and real-time data streaming architectures—that enable autonomous AI agents to access data, invoke analytical methods, and control laboratory systems.
Ensure Architecture4Insight serves as the enabling technical foundation across all Data Foundry pillars: deploying Methods4Insight’s analytical models as production APIs, integrating Scale4Insight’s real-time instrument data streams, and embedding Preparedness4Insight’s governance and metadata standards into platform design.
Design and implement workflow orchestration systems (Prefect, Airflow, Nextflow, WDL) that automate data pipelines, enable closed-loop experimentation, and provide reusable workflow templates for scientists.
Build data access and integration layers providing unified interfaces to diverse data sources (LIMS, ELNs, instruments, databases), with caching, indexing, and query optimization for interactive analytics and agent queries.
Lead platform engineering to build shared services, CI/CD automation, API gateways, and microservices architectures used across Data Foundry, establishing software engineering best practices and modern development standards.
Collaborate with Tech@Lilly Product Engineering to define pathways for transitioning prototypes to enterprise-managed production systems, establish SLAs, and represent Data Foundry in enterprise architecture forums.
Build, mentor, and help develop a high-performing platform engineering team of architects, software engineers, and DevOps specialists, fostering a culture of technical excellence and continuous learning.
Develop a multi-year roadmap for cloud platforms and infrastructure aligned with Data Foundry strategy, monitoring emerging technologies and establishing KPIs for platform performance, cost efficiency, and scientist satisfaction.

Basic Requirements

MS/Ph.D. in Computer Science, Bioinformatics, Computational Biology, or related field, OR M.S. with equivalent experience in platform engineering and scientific software.
6+ years of experience in cloud platform architecture, scientific software engineering, or research informatics, with at least 3 years in pharmaceutical, biotechnology, or life sciences industry.

Additional Preferences

Proven track record leading platform engineering or infrastructure teams (6–10+ professionals) delivering production systems.
Deep expertise in cloud-native architecture on AWS, Azure, or GCP including infrastructure-as-code, containerization, orchestration, and security.
Strong software engineering skills with experience in multiple programming languages and modern development practices.
Experience building APIs, microservices, and integration layers for complex scientific or technical systems.
Demonstrated ability to translate scientific requirements into technical architecture and scalable platform solutions.
Excellent communication skills with ability to explain technical concepts to scientists, collaborate with IT organizations, and influence stakeholders.
Experience with AI agent infrastructure, autonomous system platforms, or building APIs that AI/ML systems invoke programmatically.
Hands-on experience with Model Context Protocol (MCP) servers, LangChain, or similar frameworks for AI agent tool integration.
Deep understanding of workflow orchestration tools (Nextflow, Prefect, Airflow, WDL, Snakemake) and experience building automated scientific pipelines.
Experience with genomics, proteomics, or bioinformatics platforms and understanding of scientific data characteristics.
Familiarity with LIMS, ELN systems, and laboratory automation data integration patterns.
Track record of founding or building platforms from ground up, not just maintaining existing systems.
Experience with data governance, semantic modeling, ontologies, and metadata frameworks in scientific contexts.
Strong mentorship capabilities with passion for developing engineering talent and building collaborative teams.
Entrepreneurial mindset with ability to operate in ambiguous, fast-paced research environments.

Additional Information
Physical Demands/Travel:
The physical demands of this job are consistent with an office environment. This position will require travel (~15–20%) to collaborate with teams across multiple Lilly sites and occasional external conferences.
Work Environment
This position’s work environment is primarily in an office with computational resources, with regular interaction with laboratory environments to understand data generation and system integration requirements.
Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.
Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.
Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women’s Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.
Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is
$193,500 - $283,800
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).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.
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