Automation Scientist Jobs in Indiana (NOW HIRING)

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work-but it's work worth doing. If you're driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.
Organization Overview
Lilly Small Molecule Discovery is an organization purpose-built to create molecules that make life better for people. 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. Scale4Insight is the laboratory automation team within the Data Foundry function, responsible for deploying and scaling automation solutions that generate high-quality scientific data across Lilly research sites.
Role Summary
The Lab Automation Scientist will own the operation, development, and improvement of laboratory automation systems at the Indianapolis site, within the Scale4Insight team of the Data Foundry. This role combines hands-on responsibility for automation platforms with deep collaboration with pharmacologists, synthetic chemists, analytical scientists, and the Global Sample Management Center, translating scientific and operational needs into robust, scalable automated workflows. The individual will ensure platforms consistently deliver high-quality, reproducible data, while actively partnering with scientists and sample management operations to identify and implement new automation opportunities across the broader Indianapolis laboratory environment. The ideal candidate combines practical automation expertise with genuine scientific curiosity, someone who understands not only how the systems run, but what biology and chemistry they are trying to accomplish.
Responsibilities
Safety, Quality and Compliance - Make Safety the Foundation of Every Experiment

• Maintain safety as the top priority in all laboratory and automation work, including proper identification and handling of chemical and biological materials that pose potential risks to health, safety, or the environment.
• Maintain detailed, prompt, and compliant documentation of platform configurations, experimental procedures, maintenance activities, and outcomes.

Platform Operations and Technical Ownership - Deliver Consistent Performance and Reliability

• Own the day-to-day operation and maintenance of laboratory automation systems supporting molecular pharmacology, small molecule chemistry, and Global Sample Management Center workflows.
• Develop, optimize, and validate automated methods and workflows; maintain SOPs, maintenance logs, and method in accordance with internal standards.
• Drive root cause analysis and troubleshooting of automation issues; perform hands-on repairs and adjustments for routine hardware and software problems, and coordinate with vendors for corrective and preventive maintenance when required.
• Act as the primary automation point of contact for supported scientific teams, providing real time support and training on platform operation, standard processes, and data interpretation.
• Collaborate with the Scale4Insight team across sites to share methods, adopt proven solutions, and contribute to a unified automation strategy.

Workflow Development and Scientific Collaboration - Understand the Science, Extend the Impact

• Partner with pharmacologists, synthetic chemists, analytical scientists, and Global Sample Management Center operations to understand their research and operational needs and translate requirements into practical automation solutions.
• Map existing manual processes and find opportunities for automation across the Indianapolis site, assessing readiness and proposing solutions aligned with team priorities and scientific objectives.
• Support the design and execution of automated biochemical and cell-based assay workflows, compound profiling campaigns, small molecule chemistry experiments, and sample management operations, ensuring data quality and reproducibility standards are met.
• Contribute to the definition of data generation standards that enable effective data analysis and the training of predictive models and AI tools.

Data and Digital Integration - Connect Automation to Data and Science

• Ensure effective integration of automation platforms with compound management systems, LIMS, ELN, and downstream data pipelines, including connections to data management and AI/ML tools.
• Champion the adoption of AI/ML tools and digital workflows within the platform environment, finding opportunities to enhance automation capabilities, improve data quality, and accelerate scientific decision-making.
• Develop scripts or configuration tools (e.g., Python, C#) to extend platform capabilities and enable new workflow possibilities.
• Maintain accurate technical documentation for all supported systems, methods, and integrations.

Basic Qualifications

• B.S. or M.S. in Chemistry, Biochemistry, Pharmacology, Chemical Engineering, or a closely related discipline. A strong scientific understanding of the workflows being automated is essential, whether that comes from a science or an engineering background.
• 2+ years of hands-on experience in laboratory automation in a pharmaceutical, biotech, or drug discovery environment.
• Demonstrated ability to program and troubleshoot automated workflows on liquid handling or integrated robotic platforms.

Additional Skills / Preferences

• Practical understanding of molecular pharmacology, small molecule chemistry, analytical chemistry, or sample management workflows, and the ability to engage credibly with research scientists and operations teams.
• Experience supporting automation in a molecular pharmacology, drug discovery, or sample management context, including biochemical and cell-based assay workflows and compound handling operations.
• Experience with low-volume dispensing technologies and analytical instrumentation common in drug discovery.
• Scripting or programming skills (Python, C#, or equivalent) for workflow automation or data integration.
• Experience integrating automation platforms with compound management tools, LIMS, or ELN.
• Strong collaborative skills and the ability to align technical solutions with scientific goals.
• Effective English-language written and verbal communication skills.
• Ability to manage automation projects from requirements through commissioning, including vendor coordination.
• Demonstrated scientific curiosity, initiative, and a solutions-oriented mindset with a disciplined approach to safety and documentation.
• Proven ability to work effectively in a multidisciplinary, multi-site, international team environment.
• Views personal success in the context of team success.

Additional Information
Travel Percentage
10-20%
Work Environment / Physical Demands
This role is primarily laboratory-based, requiring hands-on work with automated instrumentation, robotics, and chemical or biological reagents in a research laboratory setting. Standard personal protective equipment is required. The scientist may work across multiple lab spaces and will engage regularly with pharmacology, chemistry, and sample management teams in collaborative environments.
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 (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women's Initiative for Leading at Lilly (WILL).
Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is
$65,250 - $148,500
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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