Staff Software Engineer, LIMS

San Diego Stealth Startup; San Diego (CA); On-site; USD 174,000 - 185,000; Full time

Job summary

San Diego Stealth Startup in San Diego, CA is seeking a technical leader to own the LIMS implementation across lab workflows, connecting sample tracking to automation and instrumentation.

You will define requirements with scientists and operations, build and configure the system, ensure data lineage, and meet 21 CFR Part 11 audit requirements. This role offers impact and collaboration with automation and lab teams in a regulated production environment.

Qualifications

• 7+ years building software for clinical or molecular diagnostics labs.
• Hands-on LIMS experience - customization, extension, and integration with lab instrumentation.
• Sample-tracking data-model experience for high-throughput complex laboratory workflows; multi-step, multi-instrument, batch-level QC gates, per-sample lineage, reagent lot tracking.
• Full stack programming experience with UI, APIs, and backend databases; git-based workflows and CI/CD in a validated system.
• Regulated-environment experience (21 CFR Part 11, ISO 13485, ISO 15189, CAP/CLIA, or GxP).
• BS or MS in Computer Science, Bioengineering, or related field or equivalent industry experience.

Responsibilities

• Build out and extend the LIMS; ensure workflows are defined and the LIMS is the source of truth for every sample’s state.
• Develop the integration layer between LIMS and lab-automation devices; worklist generation and step logging back to LIMS.
• Model the sample-preparation-assay execution-analysis-traceability chain for high-throughput workflows.
• Own the data model and sample chain-of-custody used by downstream systems.
• Ensure every step is recorded to meet 21 CFR Part 11 audit requirements.
• Collaborate with the Director of Lab Automation on software-hardware interfaces.

Skills

LIMS development

Full stack development

CI/CD

Regulated software

Communication

Education

BS/MS in CS or related field

Tools

Senaite

LabKey

Benchling

LabWare

STARLIMS

LabVantage

Sapio

Job description

Location: San Diego, CA

Job Type: Full-Time

Salary: $174,000 - $185,000

Position Overview:

We're seeking a technical leader to own the implementation of our LIMS platform, connecting sample tracking to lab automation and instrumentation across laboratory workflows. You'll own the LIMS implementation end to end: working with laboratory scientists, clinical operations, and the automation team to define requirements, then building and configuring the system to match. You'll connect LIMS to lab instruments, automation devices, and other internal systems, and own the sample-tracking data model that everything downstream depends on.

You'll need to be a highly effective communicator, comfortable sitting with lab scientists and automation engineers to translate how they work into software, rather than just taking a spec and building to it. Deep hands-on LIMS experience in clinical or molecular diagnostics labs is required; curiosity and fast learning matter just as much, since this role means going deep on new lab technologies as they come up.

This role is a unique opportunity to own a central piece to the overall success of the company.

Responsibilities:

• Build out and/or extend the LIMS. Ensure that the LIMS supports straightforward definition and use of workflows, so LIMS is the source of truth for every sample’s state through the lab.
• Build the integration layer between LIMS and the lab-automation devices - worklist generation, step logging back to LIMS, error capture, reagent lot tracking (lot ID, expiration, usage per sample).
• Model the sample - preparation - assay execution - analysis - results traceability chain for high-throughput laboratory workflows.
• Own the data model and sample chain-of-custody contract that downstream systems (ordering systems, analysis orchestration, reporting portals) rely on.
• Ensure every step is recorded to meet 21 CFR Part 11 audit requirements.
• Work with the Director of Lab Automation on the software - hardware interfaces.
• Interact with lab and other end users to map out requirements and priorities and ensure that user acceptance criteria are met.
• Contribute to CI/CD, code review, and testing practices for regulated systems.

Qualifications:

Required:

• 7+ years building software for clinical or molecular diagnostics labs.
• Hands-on LIMS experience - customization, extension, and integration with lab instrumentation. Direct experience with at least one commercial or open-source LIMS (e.g. Senaite / Bika, LabKey, OpenSpecimen, Benchling, LabWare, STARLIMS, LabVantage, or Sapio) or direct experience developing a custom LIMS used with a high-volume production assay.
• Sample-tracking data-model experience for high-throughput complex laboratory workflows; multi-step, multi-instrument, batch-level QC gates, per-sample lineage, reagent lot tracking.
• Full stack programming experience with modern programming languages and best practices, spanning the UI, APIs, and backend databases along with git-based workflows and CI/CD in a validated system
• Regulated-environment experience, e.g. 21 CFR Part 11, ISO 13485, ISO 15189, CAP / CLIA, or GxP.
• BS or MS in Computer Science, Bioengineering, or a related field or equivalent industry experience. Track record with production systems weighs more than credentials.

Nice to have:

• Comfortable with lab-automation APIs, e.g. Hamilton STAR, SPT Firefly, Thermo KingFisher, etc. You talk to them; you don't need to script the methods.
• Experience with HL7 v2, FHIR, LIS, ASTM E1394, or IHE profiles for lab / EMR interoperability.
• Familiarity with cloud (AWS, Azure, or GCP) providers and services available — enough to work with cloud-hosted services.

We are an equal opportunity employer. We thrive on diversity and collaboration.