Scientific Software Developer Jobs in Boston, MA

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.

JOB DESCRIPTION

Location:San Diego, CA; San Francisco, CA; Boston, MA; Louisville, CO; Indianapolis, IN

Lilly Small Molecule Discoveryis purpose-built to create molecules that make life better for people.Discovery Technology and Platforms (DTP)accelerates molecule discovery by building optimized foundational platforms, streamlining lab operations through advanced technologies and data connectivity, and investing in novel capabilities.

Data Foundryis a multidisciplinary team within DTP that enables AI-native drug discovery through four integrated pillars:Architecture4Insight(data infrastructure and scientific software),Methods4Insight(analytical and computational methods),Automation & Scale4Insight(lab automation and agentic workflows), andPreparedness4Insight(data governance and readiness). These pillars empower every Lilly scientist to make optimal decisions by providing seamless access to data, insights, and AI-driven capabilities-serving both human scientists and autonomous AI agents.

We are seekingScientific Software Developersat multiple levels to build the data infrastructure, scientific tools, and lab automation integrations that power AI-native drug discovery. You will work directly with front-line discovery scientists and data scientists to translate their needs into fit-for-purpose prototypes, data pipelines, APIs, and workflow tools-then hand off mature solutions toTech@Lillyfor enterprise scaling and maintenance if and when needed.

This role is anchored inArchitecture4Insightwith close collaboration acrossMethods4InsightandAutomation & Scale4Insight. You will build the scientific software that other teams-including the Frontier AI group's autonomous agents-consume. Some developers will specialize inlab automation software: building the code that interfaces with physical instruments, robotic platforms, and scheduling systems to enable Scale4Insight's closed-loop experimentation.

• 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.

• 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.

• 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, Schrodinger, 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.

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 Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women's Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.

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

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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