We are seeking a Scientific Software Developer to build the software systems that power AI-native drug discovery. You will work directly with front-line discovery scientists to translate their needs into fit-for-purpose prototypes, data pipelines, APIs, MLOps infrastructure, agentic platform components, and lab automation integrations.

This role works across Architecture4Insight , Methods4Insight , and Automation & Scale4Insight . A defining aspect is Data Foundry’s prototype-to-production operating model : you will rapidly build and validate solutions with scientists, then hand off mature prototypes to Tech@Lilly for enterprise scaling and maintenance-keeping you focused on innovation and the next high-impact problem.

Responsibilities

Scientific Data Pipelines, APIs & LIMS

• Design, build, and maintain data processing pipelines for complex scientific datasets (chemical, biological, HTE, and automation-generated data), ensuring FAIR compliance and machine-actionability.
• Develop RESTful APIs and microservices providing unified programmatic access to LIMS, ELNs, instruments, data warehouses (Postgres, Redshift, Snowflake), and analytical databases.
• Support continuous improvement of LIMS and adjacent systems to meet evolving scientific workflows, security, and scalability standards.

MLOps & Model Operationalization

• Build ML deployment pipelines-experiment tracking, model versioning (MLflow, W&B), containerized serving, monitoring, and automated retraining.
• Implement model observability: drift detection, performance alerting, and lifecycle management.
• Collaborate with Methods4Insight to operationalize cheminformatics, statistical, and AI/ML models as production APIs.

Agentic Platforms & AI Agent Infrastructure

• Develop agent-ready APIs with structured error handling, audit trails, and monitoring supporting agent autonomy and human oversight.
• Contribute to MCP servers or similar frameworks exposing Data Foundry capabilities to AI agents.
• Build software enabling closed-loop experimentation: agents design, automation executes, data flows back, models update.

Automation Software & Lab Integration

• Build integrations connecting lab automation equipment, scheduling systems, and instrument data streams to Data Foundry’s infrastructure with proper metadata and traceability.
• Create modular, reusable automation workflow components scientists can configure without writing code.

Scientific Prototyping & Tech@Lilly Handoff

• Work directly with bench scientists to rapidly prototype custom applications, dashboards, and workflow tools to improve scientist’s experience and efficiency
• Validate prototypes through iterative scientist feedback, then partner with Tech@Lilly to hand off for enterprise scaling with defined transition criteria and documentation.

Cloud Infrastructure & DevSecOps

• Build and operate cloud-native components (AWS, Azure, or GCP) supporting containerized workflows (Kubernetes/Docker), infrastructure-as-code, CI/CD, and workflow orchestration (Prefect, Airflow, Nextflow).
• Apply DevSecOps standards including security scanning, code review, and automated testing.

• B.S./M.S/Phd. in Computer Science, Bioinformatics, Computational Biology, Cheminformatics, Chemistry, Biology, Biomedical Engineering, or related STEM field.
• BS (with 10+years), MS (with 5+ years) or Phd (1+ year) of scientific software development experience, with understanding of experimental data types and scientific workflows.
• Proficiency in Python and at least one additional language (Java, C#, Go, TypeScript, or Rust); strong SQL skills.
• Experience building RESTful APIs, data pipelines, and/or microservices for scientific or technical applications., * Pharmaceutical or biotech research industry experience, particularly in discovery workflows for biology, chemistry, biochemistry or automation.
• MLOps tooling: experiment tracking (MLflow, W&B), model registries, model serving, monitoring/drift detection.
• Familiarity with cloud platforms (AWS, Azure, or GCP), containerization (Docker/Kubernetes), and Git.
• Strong communication skills with a track record of productive scientist collaboration.
• Exposure to AI agent infrastructure, MCP frameworks, or building APIs that AI/ML systems invoke programmatically.
• Experience integrating lab automation systems with digital platforms or AI-driven workflows.
• Hands-on experience with cheminformatics tools (RDKit, Schrödinger, MOE) or bioinformatics platforms.
• Experience with cheminformatics tools (RDKit, Schrödinger, MOE) or bioinformatics platforms
• Data warehousing experience (Postgres, Redshift, BigQuery, Snowflake) and scientific data standards/ontologies.
• LIMS/ELN experience (e.g., Benchling) and laboratory instrument integration.
• Workflow orchestration (Prefect, Airflow, Nextflow, WDL), CI/CD, and Linux/bash scripting.
• Strong learning agility-willingness to step outside comfort zone and adopt new technologies to get the job done.

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is

$151,500 - $244,200

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.

WeAreLilly

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.