Advisor - Lab Automation Software Engineer
Company websitelilly.com (Eli Lilly and Company, opens in new tab)
Base salary $157,500 to $253,000
Employer-published annual base salary, USD. Advertised base range in San Diego, CA
You apply on the employer's own site. Six Figure Work does not handle applications.
- LocationSan Diego, CA
- WorkplaceWorkplace not stated
- Status at last checkSource accepting applications when checked
- Last checked (4 min ago) · observed since
About this job
At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.
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.
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 (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).
Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is
$157,500 - $253,000Full-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
Source: Eli Lilly and Company on Workday · View original posting (opens in new tab)
Pay in context
This role's base floor ($157,500) is above 48% of the 11,687 Software Engineering roles nationwide listed on this site; 8 others list the same floor. Their median floor is $160,000; the middle half runs from $136,500 to $190,800.
Only jobs on this site count, and each one publishes a base salary of $100,000 or more, so this compares six-figure jobs with each other, not with the whole market. Computed Nov 7, 2026.
This listingAdvisor - Lab Automation Software Engineer$157,500 to $253,000
Senior Director, Drug Safety Operations (remote)$160,500 to $259,600
Senior Director, Portfolio Strategy, Analytics & Enablement, Cardiometabolic Research$160,500 to $235,400
Functional Service Team Executive/Senior Director, Clinical Delivery Capabilities – Exploratory Medicine Pharmacology (EMP)$160,500 to $235,400
Sr Director - Enterprise Connectivity & Network Services$159,000 to $233,200
Advisor - Lab Automation Software Engineer, AI-Integration$157,500 to $231,000
Director/Sr. Director - Medicinal Chemistry (synthetic macrocycles)$163,500 to $239,800
Chart as a table
| Role | Published base |
|---|---|
| Advisor - Lab Automation Software Engineer (this listing) | $157,500 - $253,000 |
| Senior Director, Drug Safety Operations (remote) | $160,500 - $259,600 |
| Senior Director, Portfolio Strategy, Analytics & Enablement, Cardiometabolic Research | $160,500 - $235,400 |
| Functional Service Team Executive/Senior Director, Clinical Delivery Capabilities – Exploratory Medicine Pharmacology (EMP) | $160,500 - $235,400 |
| Sr Director - Enterprise Connectivity & Network Services | $159,000 - $233,200 |
| Advisor - Lab Automation Software Engineer, AI-Integration | $157,500 - $231,000 |
| Director/Sr. Director - Medicinal Chemistry (synthetic macrocycles) | $163,500 - $239,800 |
Observed changes
- First observed on the employer's board
- Began meeting the published-salary criteria
- Observed since
- Employer-stated posting date
- 2026-11-02
Where this pay comes from
Location as the employer wrote it: US, San Diego CA
$157,500 - $253,000
- Method
- Employer text, read with fixed rules and re-verified
- Checked
- Rule set
- us-base-v2
The pay passage appears in the employer's own job text. Fixed, deterministic rules located it, and the passage below was checked against the stored copy of the posting.
What we verified
- The pay figures come from the employer's own listing, quoted exactly above.
- The pay is an annual base salary in US dollars with a minimum of at least $100,000.
- The role was publicly listed on the employer's job board when last checked.
We do not verify what the employer will actually offer, whether the employer is still recruiting for the role, or anything beyond what the employer published. Full methodology.