Senior Software Engineer Lab Automation

Roche; Penzberg; On-site; EUR 160,000 - 224,000; Full time

Job summary

Roche Basel is seeking a Senior Lab Automation Software Engineer to bridge software and hardware in the lab, delivering scalable automation solutions. You will collaborate with automation scientists to design high-throughput workflows, integrate instruments, and build data-driven systems that enhance experimental throughput and reliability.

Ideal candidates have 5+ years in software/hardware integration, strong C# or Python skills, and a background in lab workflows, CAD prototyping, and

Qualifications

• At least 5 years of software engineering and hardware integration experience.
• Experience programming lab automation platforms and integrating robotic manipulators.
• Proficiency in C# or Python for software integration.
• Familiarity with molecular biology, biochemistry, or wet lab workflows.
• Prototyping in CNC milling, laser cutting, and CAD.
• Strong communication for collaboration with scientists and engineers.
• Experience using APIs/SDKs to interact with lab software ecosystems.
• Experience designing workflow orchestration or scheduling systems.

Responsibilities

• Design, program, and troubleshoot high-throughput lab workflows.
• Build orchestration systems and hardware abstraction layers.
• Implement logging, metrics, and alerts with robust root-cause analysis.
• Create a digital lab representation with sample identity and instrument state.
• Connect instruments via APIs and integrate with LIMS/ELNs.
• Collaborate with software, automation scientists, and hardware engineers.

Skills

C#

Python

APIs/SDKs

Lab automation

CNC milling

Laser cutting

CAD

OpenCV

YOLO

SAM

Cloud infrastructure

Digital twin

Vision models

AI/ML models

Reinforcement learning

Imitation learning

Robotics

Task-and-motion planning

Sensors

Microcontrollers

Job description

At Roche you can show up as yourself, embraced for the unique qualities you bring. Our culture encourages personal expression, open dialogue, and genuine connections, where you are valued, accepted and respected for who you are, allowing you to thrive both personally and professionally. This is how we aim to prevent, stop and cure diseases and ensure everyone has access to healthcare today and for generations to come. Join Roche, where every voice matters.

The Position

Advances in AI, data, and computational sciences are transforming drug discovery and development. Roche’s Research and Early Development organisations at Genentech (gRED) and Pharma (pRED) have demonstrated how these technologies accelerate R&D, leveraging data and novel computational models to drive impact. Seamless data sharing and access to

models across gRED and pRED are essential to maximising these opportunities. The newComputational Sciences Center of Excellence (CoE) is a strategic, unified group whose goal is to harness this transformative power of data and Artificial Intelligence (AI) to assist our scientists in both pRED and gRED to deliver more innovative and transformative medicines for patients Worldwide.

Within the CoE organisation, the Data and Digital Catalyst (DDC) organisation drives the modernisation of our computational and data ecosystems and integration of digital technologies across Research and Early Development to enable our stakeholders, power data-driven science and accelerate decision-making.

As a senior lab automation software engineer, you will be the essential link to the automation scientists in the lab. Using your background in both software development and hardware integration, you will work with a team of software-focused engineers to build, test and do what is needed to bring the software and hardware layers into production.

The Opportunity

To excel in this role, you will bridge the gap between complex software engineering and laboratory research in drug discovery through the following responsibilities:

• Design, program and troubleshoot high-throughput lab workflows.
• Build orchestration systems, hardware abstraction layers, and instrument drivers that manage retries and allow unattended operation.
• Implement logging, metrics, and alerts across hardware and software to identify failures. Fix root causes using software or vision models instead of relying on manual workarounds or vendor support.
• Build systems to maintain a digital representation of the lab, including sample identity, instrument state, and resource availability. Connect instruments via APIs and integrate with LIMS and ELNs.
• Manage hardware requirements, site constraints, reagent selection, and work cell integration from initial design to deployment.
• Work directly with software engineers, automation scientists, and hardware engineers to turn scientific processes into technical architectures.

Who You Are

• You have 5+ years of experience in software engineering and hardware integration.
• Experienced in programming commercial liquid-handling or laboratory automation platforms and integrating robotic manipulators.
• Proficient in C# or Python for building software and integration frameworks.
• Familiar with molecular biology, biochemistry, or wet lab workflows to help translate scientific needs into engineering solutions.
• Prototyping design experience, including CNC milling, laser cutting, and CAD.
• A clear communicator who collaborates with scientists and multidisciplinary teams to build complete solutions.
• Skilled at using APIs and SDKs to interact with complex laboratory software ecosystems.
• Experienced in designing workflow orchestration or scheduling systems that manage shared resources, dependencies, and priorities.

Preferred skills and experience

• Skilled with computer vision models (such as OpenCV, YOLO, or SAM) for automated error handling and object or anomaly detection.
• Experienced in training, evaluating, or adopting AI/ML models, including reinforcement or imitation learning for robotics.
• Capable of building and evaluating AI-enabled systems, defining evals, establishing guardrails for determinism versus nondeterminism, and measuring reliability.
• Knowledgeable about sensors, microcontrollers, and task-and-motion planning.
• Familiar with cloud infrastructure and digital twin simulation.

A cover letter is not necessary, you will be required to fill a questionnaire.

Where pay transparency applies, details are provided based on the primary posting location. For this role, the primary location is Basel. If you are interested in additional locations where the role may be available, we will provide the relevant compensation details later in the hiring process.

Who we are

A healthier future drives us to innovate. Together, more than 100’000 employees across the globe are dedicated to advance science, ensuring everyone has access to healthcare today and for generations to come. Our efforts result in more than 26 million people treated with our medicines and over 30 billion tests conducted using our Diagnostics products. We empower each other to explore new possibilities, foster creativity, and keep our ambitions high, so we can deliver life-changing healthcare solutions that make a global impact.

Let’s build a healthier future, together.

Roche is an Equal Opportunity Employer.