Nextflow Jobs in Indiana (NOW HIRING)

Job Summary:
Eli Lilly and Company is a global healthcare leader headquartered in Indianapolis, Indiana, dedicated to making life better for people around the world. They are seeking a Scientific Software Developer for their Data Foundry team, which focuses on AI-native drug discovery by developing software systems that support scientific data pipelines, APIs, and lab automation integrations.
Responsibilities:
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
Qualifications:
Required:
• 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.
Preferred:
• 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.
• 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.
Company:
We're a medicine company turning science into healing to make life better for people around the world. Founded in 1876, the company is headquartered in Indianapolis, USA, with a team of 10001+ employees. The company is currently Late Stage.