Automation Engineer II

Amyris, Inc.; Berkeley (CA); On-site; USD 103,000 - 131,000; Full time

Job summary

Amyris, Inc. is seeking an Automation Engineer II to support and enhance automated laboratory workflows in Emeryville, CA. You will work with liquid handlers, instruments, and scientists to build high-throughput methods from design to analysis.

The role emphasizes hands-on hardware, software troubleshooting, scripting growth, and collaboration with cross-functional teams to improve reliability and throughput on a production-scale synthetic biology platform.

Qualifications

• Bachelor’s degree in a related scientific or engineering field or equivalent
• 2–3 years of experience in laboratory automation or related field
• Hands-on experience with automated laboratory instrumentation and liquid-handling platforms
• Exposure to scheduling/orchestration platforms such as Biosero Green Button Go, Agilent VWorks, HighRes Cellario, or similar
• Basic scripting or programming concepts (Python, C#, VBScript) with interest to grow

Responsibilities

• Develop, test, and deploy automated laboratory methods on liquid handlers and platforms
• Translate manual protocols into reliable automated workflows
• Troubleshoot instrument, software, labware, and workflow issues
• Coordinate with vendors for maintenance and qualification activities
• Create and maintain technical documentation and SOPs
• Identify bottlenecks and contribute to improvements for system reliability and uptime
• Collaborate with engineers, scientists, and users across teams

Skills

Laboratory automation

Troubleshooting

Scripting/Programming

Communication

Team collaboration

Education

Bachelor’s degree in Bioengineering/biomedical engineering/related field

Tools

Beckman Coulter Biomek

Labcyte/Beckman Echo

Agilent VPrep

Dynamic Devices Lynx

Job description

At Amyris, we value that everyone’s career journey is unique and authentic to who they are. If this role excites you, we encourage you to apply and grow alongside us! You may be just the right candidate for this or other open roles.

Ready to put your hands-on laboratory automation experience to work while growing your programming skills?

Join Amyris as an Automation Engineer II and help scientists work faster and more reliably by supporting, troubleshooting, and improving automated laboratory workflows. You’ll work directly with liquid handlers, laboratory instrumentation, scientists, and experienced automation engineers to develop reliable, high-throughput workflows—from genetic design through screening and analysis.

If you enjoy solving practical hardware and workflow challenges and want to build your scripting and programming capabilities, this is an opportunity to make a visible impact on a production-scale synthetic biology platform.

*This is a fully onsite role based in Emeryville, CA.

Responsibilities

• Method & Workflow Development: Support the development, modification, testing, and deployment of automated laboratory methods on liquid handlers and other laboratory automation platforms. Execute defined method-development activities independently and work with more experienced automation engineers on complex or integrated workflows.
• Laboratory Workflow Automation: Work with automation engineers, scientists, and laboratory users to understand manual laboratory protocols and help translate them into reliable automated workflows using established platforms, standards, and development practices.
• Troubleshooting & Technical Support: Provide day-to-day support for laboratory automation systems. Troubleshoot routine to moderately complex issues involving instrumentation, automation software, labware, consumables, and liquid-handling methods. Escalate complex, unfamiliar, or cross-system issues when additional technical expertise is required.
• Maintenance & Vendor Coordination: Support routine instrument maintenance, calibration, equipment qualification activities, and troubleshooting. Coordinate with equipment vendors and service providers as needed under established support processes.
• Documentation: Develop and maintain method documentation, standard operating procedures, user guides, troubleshooting instructions, and other technical documentation using established team standards.
• Continuous Improvement: Contribute to identifying operational bottlenecks, recurring automation issues, and opportunities to improve system reliability, assay execution, and automation uptime. Participate in implementation and testing of improvement efforts.
• Team Collaboration & Knowledge Sharing: Participate in technical discussions, share troubleshooting findings, seek input when appropriate, and collaborate with automation engineers, scientists, laboratory staff, vendors, and other cross-functional partners.

Basic Qualifications

• Bachelor’s degree in Bioengineering, Biomedical Engineering, Molecular Biology, Biotechnology, a related scientific or engineering field, or an equivalent combination of education and practical experience.
• Approximately 2–3 years of relevant experience in laboratory automation, laboratory instrumentation, engineering, biotechnology, pharmaceutical development, or a related technical environment.
• Hands‑on experience operating, supporting, programming, or troubleshooting automated laboratory instrumentation. Experience with liquid‑handling platforms is strongly preferred. (e.g., Beckman Coulter Biomek, Labcyte/Beckman Echo, Agilent VPrep, Dynamic Devices Lynx).
• Exposure to laboratory scheduling or orchestration platforms such as Biosero Green Button Go, Agilent VWorks, HighRes Cellario, or similar systems.
• Basic familiarity with scripting or programming concepts used in automation environments, such as Python, C#, VBScript, or similar languages, with an interest in developing these skills further.
• Ability to apply systematic troubleshooting methods to routine and moderately complex hardware, software, labware, and workflow‑related problems.
• Ability to communicate technical information clearly, document work effectively, collaborate with laboratory users and engineering colleagues, and seek guidance when appropriate.
• Demonstrated ability to learn new technologies, incorporate feedback, and develop increasing technical independence over time.

Preferred Qualifications

• Experience supporting automation hardware, including electronics troubleshooting and repair.
• Interest or experience in mechanical troubleshooting, CAD, 3D printing, fabrication, electronics, or development of simple laboratory fixtures is a plus.
• Familiarity with standard molecular biology and synthetic biology workflows (e.g., PCR setup, DNA assembly, transformations, NGS library prep, microplate assays, or cell culture plating).
• Exposure to laboratory data systems, LIMS, file‑based data exchange, or automated transfer of instrument and workflow data.
• Familiarity with Git or another version‑control system for scripts, configuration files, or automation methods.

The salary range for this role is: $ 103,000 to $131,000.

As a VEVRAA Federal Contractor, Amyris is an equal opportunity employer and all qualified applicants will receive consideration for employment without regard to race, sex, color, religion, sexual orientation, gender identity, national origin, disability status, protected veteran status, or any other characteristic protected by law. Amyris complies with applicable state and local laws governing nondiscrimination in employment.

Amyris is committed to fair and equitable compensation practices.Salary offers are made based on internal equity and market analysis, and will vary based on the candidate’s skills, depth of experience and specific work location.

Amyris is committed to providing a diverse array of inclusive benefits and perks to support employees and their families’ wellbeing including access to robust healthcare, mental wellness benefits, family leave, discounted fitness memberships, education reimbursement, flexible paid time off, 17 paid holidays, 10 paid sick days, and additional paid time off including 3 volunteer days, and bereavement.

What may Candidates Expect from Amyris?

At Amyris, we strive to provide a transparent and professional hiring experience. Our interview process typically includes a combination of in-person meetings and phone conversations. Genuine job offers are always communicated by an authorized member of our Human Resources team before being sent via email. Please note that all official communication from Amyris employees will come from an email address ending in “@amyris.com” or from \"[e-mail]\".

Amyris is committed to providing a diverse array of inclusive benefits and perks to support employees and their families’ wellbeing including access to robust healthcare, mental wellness benefits, family leave, discounted fitness memberships, education reimbursement, flexible paid time off, 17 paid holidays, 10 paid sick days, and additional paid time off including 3 volunteer days, and bereavement.

Voluntary Self-Identification

For government reporting purposes, we ask candidates to respond to the below self-identification survey. Completion of the form is entirely voluntary. Whatever your decision, it will not be considered in the hiringprocess or thereafter. Any information that you do provide will be recorded and maintained in aconfidential file.

As set forth in Amyris, Inc.’s Equal Employment Opportunity policy,we do not discriminate on the basis of any protected group status under any applicable law.

If you believe you belong to any of the categories of protected veterans listed below, please indicate by making the appropriate selection.As a government contractor subject to the Vietnam Era Veterans Readjustment Assistance Act (VEVRAA), we request this information in order to measurethe effectiveness of the outreach and positive recruitment efforts we undertake pursuant to VEVRAA. Classification of protected categoriesis as follows:

A \"disabled veteran\" is one of the following: a veteran of the U.S. military, ground, naval or air service who is entitled to compensation (or who but for the receipt of military retired pay would be entitled to compensation) under laws administered by the Secretary of Veterans Affairs; or a person who was discharged or released from active duty because of a service‑connected disability.

A \"recently separated veteran\" means any veteran during the three-year period beginning on the date of such veteran's discharge or release from active duty in the U.S. military, ground, naval, or air service.

An \"active duty wartime or campaign badge veteran\" means a veteran who served on active duty in the U.S. military, ground, naval or air service during a war, or in a campaign or expedition for which a campaign badge has been authorized under the laws administered by the Department of Defense.

An \"Armed forces service medal veteran\" means a veteran who, while serving on active duty in the U.S. military, ground, naval or air service, participated in a United States military operation for which an Armed Forces service medal was awarded pursuant to Executive Order 12985.