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Job Location: Scientific Protein Laboratories - Waunakee, WI 53597

Position Type: Full Time

Job Category: Engineering

Join our team at Scientific Protein Laboratories (SPL), a world leader in biosourced pharmaceuticals, located just outside of Madison, Wisconsin in Waunakee! SPL is an innovative biopharmaceutical leader with unique products and services supporting the pharmaceutical industry globally. For over 40 years, SPL specializes in the development and cGMP compliant manufacturing of Active Pharmaceutical Ingredients (APIs).

The Automation Engineer is responsible for the development, maintenance, and troubleshooting of PLC and HMI programs for production and utility systems in a cGMP pharmaceutical manufacturing environment. This role requires meticulous attention to detail, strict adherence to programming standards (including ISA-88/S88 batch control standards), and thorough documentation practices to ensure compliance with FDA 21 CFR Part 11, data integrity requirements, and validation protocols. The Automation Engineer will focus primarily on Rockwell Automation platforms including ControlLogix, CompactLogix, PlantPAx, and FactoryTalk View SE applications. This position works cross-functionally with Production, Quality, and Engineering teams to optimize automated systems and advises on automation requirements for capital improvement projects.

• Develop, maintain, and troubleshoot PLC programs using Rockwell Automation ControlLogix and CompactLogix platforms in compliance with cGMP and FDA 21 CFR Part 11 requirements
• Design, program, and maintain HMI applications using Rockwell FactoryTalk View Site Edition (SE), ensuring strict adherence to data integrity principles (ALCOA+)
• Program and maintain PlantPAx distributed control system applications following ISA-88 (S88) batch control standards and established programming conventions
• Create and maintain accurate, revision-controlled program documentation including functional specifications, code comments, and change logs per pharmaceutical industry standards
• Document all automation work activities, troubleshooting outcomes, and system modifications in the CMMS (Fiix) to maintain comprehensive equipment history records
• Implement and validate control system modifications following established change control procedures and validation protocols (IQ/OQ/PQ)
• Troubleshoot and resolve automation system issues in a timely manner to minimize production downtime while maintaining complete documentation of all actions taken
• Collaborate with Production, Quality, and other departmental teams to identify, optimize, and resolve pain points with automated system operations
• Support process validation activities by programming recipe-based batch control systems and ensuring audit trail functionality
• Collaborate with Quality Assurance to ensure all automation changes meet regulatory requirements and pass internal/external audits
• Advise Project Engineers on automation requirements for capital projects, including recommendations for large-scale improvements, PLC hardware upgrades, and HMI system enhancements
• Maintain revision control of all PLC and HMI programs using established version control practices
• Develop standardized programming templates and reusable code modules following S88 and internal programming standards to ensure consistency across production systems
• Support maintenance technicians with troubleshooting guides and technical documentation for automated systems
• Participate in root cause analysis for automation-related deviations and implement corrective actions with appropriate documentation

• Support capital projects involving automation system installations and upgrades
• Assist with network infrastructure maintenance for industrial control systems
• Perform other duties as assigned

• Education: Required- associate’s degree in industrial Automation, Electronics Technology, Instrumentation, Computer Science, or related technical discipline
• Preferred: Bachelor’s degree in computer science, Engineering Technology, or related discipline
• Experience: Required: 3+ years of hands‑on PLC and HMI programming experience with Rockwell Automation platforms (ControlLogix, CompactLogix, FactoryTalk View SE)
• Preferred: 5+ years in pharmaceutical, API, or FDA‑regulated manufacturing environment
• Highly Preferred: PlantPAx DCS programming and configuration experience

• Required: Proficient in Rockwell Studio 5000/RSLogix 5000 for PLC programming (Ladder Logic, Structured Text, Function Block)
• Proficient in FactoryTalk View Site Edition (SE) for HMI development
• Understanding of industrial networking (EtherNet/IP, DeviceNet)
• Experience documenting work activities and equipment history in a CMMS
• Preferred: Experience with FactoryTalk Historian and FactoryTalk Batch
• Knowledge of FDA 21 CFR Part 11 compliance and data integrity requirements (ALCOA+)
• Highly Preferred: PlantPAx distributed control system programming and configuration
• Experience following ISA-88 (S88) batch control programming standards

Compensation range: $70,000-$100,000; based on experience, skills and qualifications

Our employees are our success! We recruit motivated people, recognize their contributions, and support their development to reach their full potential.

Perks include: competitive compensation; excellent benefits package - including Medical, Dental and Vision on Day 1; Life and AD&D Insurance, and Short and Long-term Disability; Health and Flexible Saving Account options; Employee Assistance Program, generous vacation; paid Holidays; 401k; advancement opportunities; team-oriented environment; community involvement; company events and more!

SPL is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to age, color, creed, disability, gender identity, national origin, protected veteran status, race, religion, sex, sexual orientation, and any other status protected by applicable local, state or federal law.