Design of a 64-Byte CAN Bus Fragmentation and Acknowledgment Protocol for DNA Extraction Instrument Controller

Modern lab automation systems are rooted primarily on embedded controllers to operate sophisticated equipment of high accuracy, reliability, and throughput. The equipment, particularly molecular diagnostics and DNA sequencing, must integrate tightly mechanical components, sensors, and controllers for efficient sample handling and processing. For this, fast and dependable communication between the central processing unit and peripheral devices such as motor controllers is necessary. While previously interfaces such as UART or USB have ensured such communication, with laboratory equipment tending to become more modular, rugged, and networked controlled, the Controller Area Network (CAN) bus has been looked upon as a viable alternative because of its fault tolerance, deterministic timing, and widespread application in industrial and automotive control systems. The move from USB to CAN in laboratory instrumentation is a signal that applications increasingly require more aggressive, scalable communications infrastructures, particularly in safety and reliability constrained situations. Such a move is accompanied by additional challenges, particularly if data payloads are greater than the standard 8-byte frame size support provided by CAN 2.0B. In such situations, higher-layer protocol must be utilized in order to control fragmentation, sequence, and acknowledgment in order to ensure complete and error-free data transfer. This thesis is conducted in collaboration with M31, a company that developes an extremely automated DNA extraction and purification platform. Within the course of updating the system, the present USB-based communication is being replaced by a CAN bus interface. The topic of this work is the development of a reliable fragmentation and acknowledgment protocol appropriate for CAN-based communication between the PC and an axis motor controller board.

Modern lab automation systems are rooted primarily on embedded controllers to operate sophisticated equipment of high accuracy, reliability, and throughput. The equipment, particularly molecular diagnostics and DNA sequencing, must integrate tightly mechanical components, sensors, and controllers for efficient sample handling and processing. For this, fast and dependable communication between the central processing unit and peripheral devices such as motor controllers is necessary. While previously interfaces such as UART or USB have ensured such communication, with laboratory equipment tending to become more modular, rugged, and networked controlled, the Controller Area Network (CAN) bus has been looked upon as a viable alternative because of its fault tolerance, deterministic timing, and widespread application in industrial and automotive control systems. The move from USB to CAN in laboratory instrumentation is a signal that applications increasingly require more aggressive, scalable communications infrastructures, particularly in safety and reliability constrained situations. Such a move is accompanied by additional challenges, particularly if data payloads are greater than the standard 8-byte frame size support provided by CAN 2.0B. In such situations, higher-layer protocol must be utilized in order to control fragmentation, sequence, and acknowledgment in order to ensure complete and error-free data transfer. This thesis is conducted in collaboration with M31, a company that develops an extremely automated DNA extraction and purification platform. Within the course of updating the system, the present USB-based communication is being replaced by a CAN bus interface. The topic of this work is the development of a reliable fragmentation and acknowledgment protocol appropriate for CAN-based communication between the PC and an axis motor controller board.