Advisor - Lab Automation Software Engineer

100 Eli Lilly and Company; San Diego (CA); On-site; USD 141,000 - 229,000; Full time

Benefits offered by this job

401(k)

Vacation benefits

Medical benefits

Flexible benefits

Job summary

Lilly seeks a Lab Automation Software Engineering Advisor at the San Diego Biotechnology Center to architect AI-integrated, closed-loop discovery systems for biotherapeutics. You will design software to orchestrate automated workflows, build data pipelines, and deploy ML models for inspection, maintenance, and optimization.

Join a team advancing AI, automation, and digital lab infrastructure to accelerate discovery with minimal human intervention, and collaborate across science and engineering

Qualifications

• PhD/MS/BS in CS/Software/Bioengineering with industry experience.
• Strong Python/SQL/JavaScript skills; ML knowledge preferred.
• Experience with automation, LIMS, cloud, and data platforms.

Responsibilities

• Architect and implement AI-integrated lab automation software.
• Build data pipelines and visualization tools for real-time lab insights.
• Develop ML models for inspection, maintenance, and optimization.
• Create digital lab infrastructure and IoT integrations.

Skills

Python

SQL

JavaScript

C#

VBA

R

C++

MATLAB

Bash

Education

Ph.D. in Computer Science or related

M.S. in Computer Science or related

B.S. in Computer Science or related

Tools

Tableau

Power BI

Spotfire

JMP

SAS

GitHub

GitLab

AWS

Azure

Benchling

LabGuru

PostgreSQL

Genedata

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. We are seeking a Lab Automation Software Engineering Advisor to join our biotherapeutics discovery automation team at the Lilly Biotechnology Center in San Diego, where you'll architect and implement revolutionary software solutions that transform how we discover life-saving biotherapeutics. As a Lab Automation Software Engineering Advisor, you'll be at the forefront of designing and building AI-integrated, closed-loop autonomous discovery ecosystem whereby intelligent systems propose hypotheses, execute experiments through advanced robotics, analyze results instantly, and iteratively refine and design the next set of experiments - all with minimal human intervention. In your role, you'll harness the latest breakthroughs in AI, machine learning, and laboratory digitalization to build software that makes our biotherapeutics discovery automation lab smarter, faster, and more innovative than ever before. If you're excited about harnessing AI and automation to solve real-world problems in drug discovery and want to be part of building the lab of the future, we want to hear from you. You will have the opportunity to: Design and develop software applications that orchestrate complex automated laboratory workflows and closed-loop learning systems. Build data pipelines and visualization tools that provide real-time insights into lab operations and experimental outcomes. Implement machine learning models for visual inspection systems, predictive maintenance, and process optimization that enhance operational efficiency. Create digital lab infrastructure including IoT integrations, digital lab twin models, and telemetry monitoring systems. Develop and maintain integrations across multiple automation schedulers, LIMS, and data platforms. Ensure robust software deployment through best DevOps practices and cloud-based solutions.

Basic Qualifications

Ph.D. in Computer Science, Software Engineering, Bioengineering/Engineering with at least three years of industry experience. M.S. in Computer Science, Software Engineering, Bioengineering/Engineering with at least 10 years of experience. B.S. in Computer Science, Software Engineering, Bioengineering/Engineering with at least 13 years of experience. Experience should include relevant industry experience, preferably in a pharmaceutical company or an automation provider.

Additional Skills/Preferences

Strong proficiency in Python, SQL, and JavaScript, with working knowledge of programing/scripting in C#, VBA, R, C++, MATLAB, and Bash. Experience with statistical analysis tools (JMP, SAS, R) and business intelligence platforms (Tableau, Power BI, Spotfire). Expertise in best DevOps practices, including database management systems (DBMS), data warehousing, software development, cloud computing platforms (AWS, Azure), and version control tools (GitHub, GitLab). Experience with lab digitalization technologies (IoT device integration, digital lab twins, automated usage and error reporting telemetry metrics) as well as autonomous lab systems and closed-loop learning frameworks is strongly preferred. Familiarity with lab data platforms including Benchling, LabGuru, PostgreSQL, Genedata, or similar LIMS/ELN systems. Strong problem-solving skills and ability to work cross-functionally with scientific and engineering teams. Background in life sciences, pharmaceutical research, or high-throughput screening environments.

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.

Employee Resource Groups

• 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 $141,000 - $228,800 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 strive to ensure our employees are part of a team that cared about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe! #WeAreLilly