Pharmaceutical Software Developer Jobs in California

Job Summary:
Eli Lilly and Company is a global leader in pharmaceutical innovation, committed to improving patient lives through scientific discovery. They are seeking Scientific Software Developers to build data infrastructure and scientific tools that facilitate AI-native drug discovery, collaborating closely with scientists to create effective software solutions.
Responsibilities:
• Design, build, and maintain data processing pipelines for complex scientific datasets (chemical, biological, High throughput experiments, 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.
• Work directly with bench scientists to understand pain points and rapidly prototype custom applications, dashboards, and workflow tools.
• Validate prototypes through iterative scientist feedback, ensuring solutions are fit-for-purpose before transition.
• Partner with Tech@Lilly Product Engineering to hand off mature prototypes for enterprise scaling, defining transition criteria, documentation standards, and SLAs.
• Build integrations connecting lab automation equipment, scheduling systems, and instrument data streams to Data Foundry’s infrastructure with proper metadata and execution traceability.
• Develop software for robotic workflow control, instrument driver interfaces, and real-time data capture from automated platforms.
• Create modular, reusable automation workflow components scientists can configure without writing code.
• Support Scale4Insight’s Agentic Lab by building software enabling seamless interfacing between automation platforms and AI-driven experimental planning.
• 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.
• Participate in agile development with iterative improvement and cross-functional collaboration.
Qualifications:
Required:
• B.S. or M.S. in Computer Science, Bioinformatics, Cheminformatics, Computational Biology, Chemistry, Biology, Biomedical Engineering, or related STEM field.
• Bachelor with 3+ years and Master with 1+ years of scientific software development, with understanding of experimental data types and scientific workflows.
• Proficiency in Python and at least one additional language (Java, C#, Go, or TypeScript); SQL skills appropriate to level.
• Qualified applicants must be authorized to work in the United States on a full-time basis. Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1.
Preferred:
• Experience (or demonstrated aptitude at junior levels) building RESTful APIs, data pipelines, and/or microservices for scientific or technical applications.
• Familiarity with cloud platforms (AWS, Azure, or GCP), containerization (Docker/Kubernetes), and Git.
• Strong communication skills and interest to collaborate with scientists and multi-functional teams.
• Pharmaceutical or biotech research industry experience, particularly in discovery workflows for biology, chemistry, or automation.
• LIMS/ELN experience (e.g., Benchling) and laboratory instrument integration.
• Experience integrating lab automation systems with digital platforms, including instrument control, robotic workflow orchestration, or scheduling systems (OPC-UA, serial/USB protocols, automation scheduling platforms).
• Data warehousing experience (Postgres, Redshift, BigQuery, Snowflake) and scientific data standards/ontologies.
• Hands-on experience with cheminformatics tools (RDKit, Schrödinger, MOE) or bioinformatics platforms (Biopython, Bioconductor, sequence analysis pipelines).
• Experience with scientific computing libraries (SciPy, NumPy) for numerical methods, ODE solvers, optimization, or PK/PD modeling workflows.
• Workflow orchestration (Prefect, Airflow, Nextflow, WDL) and CI/CD practices.
• Strong learning agility—willingness to step outside comfort zone and adopt new technologies to get the job done.
• Experience with C, C++, or other compiled languages for porting performance-critical scientific workflows; ability to profile and identify computational bottlenecks.
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.