Scientific Software Developer, Data Foundry
Company: Eli Lilly and Company
Location: San Francisco
Posted on: March 19, 2026
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Job Description:
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 Position:
Scientific Software Developer, Data Foundry Location: San Diego,
CA; San Francisco, CA; Boston, MA; Louisville, CO; Indianapolis, IN
Overview Lilly Small Molecule Discovery is 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 Foundry is 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), and Preparedness4Insight (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. Position Summary We are seeking Scientific
Software Developers at 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 to Tech@Lilly for
enterprise scaling and maintenance if and when needed. This role is
anchored in Architecture4Insight with close collaboration across
Methods4Insight and Automation & Scale4Insight . You will build the
scientific software that other teams—including the Frontier AI
group’s autonomous agents—consume. Some developers will specialize
in lab automation software : building the code that interfaces with
physical instruments, robotic platforms, and scheduling systems to
enable Scale4Insight’s closed-loop experimentation.
Responsibilities Scientific Data Pipelines & APIs 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. Scientific Prototyping & Tech@Lilly Handoff
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. 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 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. 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. Participate in agile development with iterative
improvement and cross-functional collaboration. Basic Requirements
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. Preferred
Qualifications 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. 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. WeAreLilly
Keywords: Eli Lilly and Company, San Francisco , Scientific Software Developer, Data Foundry, IT / Software / Systems , San Francisco, California
