Principal Scientist – Data Foundry Scientific Developer

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.

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.

Data Foundry is a multidisciplinary team dedicated to enabling and accelerating molecule discovery through scalable and reproducible data generation, fueled by advanced scientific programming, research informatics and automation solutions. The team also leads the design, implementation and validation of AI agent-compatible automation systems.

Position Summary: The Scientific Systems group within the Data Foundry is seeking a talented scientific programmer to join our dynamic team. This role bridges the gap between laboratory science and computational innovation, building fit-for-purpose data infrastructure and analytical pipelines that drive scientific discovery. This role will collaborate with foundational platforms and partner with Tech@Lilly and the Advanced Intelligence team (AI@Lilly) to ensure project data and software solutions are fully leveraged to facilitate scientific innovation and decision-making across the portfolio.

Key Responsibilities

• Design, develop, and maintain data retrieval, cleaning, and processing pipelines for complex scientific datasets
• Collaborate with multidisciplinary teams to translate scientific requirements into technical solutions
• Implement scalable computational workflows for chemistry and biology research applications
• Develop and optimize software tools and automation scripts to enhance research productivity
• Ensure data integrity, quality control, and reproducibility across scientific computing systems
• Participate in agile development cycles with iterative improvement and rapid prototyping
• Document technical processes and provide training support to research teams

Required Qualifications

• BS/MS in Chemistry, Biology, Biochemistry, Computational Biology, Cheminformatics, Computer Science or related field with 5+ years scientific programming experience with understanding of experimental data types and workflows
• Proficiency in multiple programming languages including Python, RESTful API, Java, C#, and SQL and Strong scientific prototyping/scripting

Preferred Qualifications

• Pharmaceutical and/or Biotech Research Industry Experience
• Python Back-end or Web development experience is highly desirable
• Hands-on experience with popular cheminformatics systems such as RDKit, Schrdinger Suite, or MOE (Molecular Operating Environment)
• Experience of integration of Benchling functions
• Experience with scientific data standards and ontologies
• Knowledge of cloud computing platforms (AWS, Azure, Google Cloud Platform)
• Familiarity with version control systems (Git) and CI/CD practices
• Experience with data visualization and analysis tools
• Background in machine learning or statistical modeling…