Building a Circaflex Ready-to-Use Control System for DNA Sequencing

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"All of this was possible for both Cyth and Nexogen because of the Circaflex Developer Suite, our off-the-shelf control system product based on NI Single-Board RIO and NI LabVIEW software. "

- Candice Garcia, Cyth Systems

The Challenge:
Controlling and maintaining an environment that requires precise temperature changes and sensor control in order to complete DNA reactions, while monitoring the process with a touch-screen human-machine interface (HMI).

The Solution:
Using Circaflex Developer Suite, which is based on NI Single-Board RIO hardware and LabVIEW software, to develop and build a system within three days that included the required sensors and a simple, straightforward HMI for system control.

Author(s):
Candice Garcia - Cyth Systems

Cyth Systems, a National Instruments Gold Alliance Partner, is a leading systems integrator and engineering firm that provides products and services to customers for automation and embedded control system solutions. National Instruments referred a life science customer, Nexogen, Inc., to us due to our expertise in complex life science applications and rapid system integration solutions. Nexogen is a privately held biotechnology company specializing in molecular diagnostics that enables rapid detection of cardiovascular, respiratory, and infectious diseases for medical, food, and veterinary applications. Their products and portable instruments are developed in hopes of diagnosing respiratory and infectious diseases early on. They needed us for reliable, cost-effective and efficient design and control of a next-generation polymerase chain reaction (PCR) machine.

PCR is a scientific process in which researchers replicate thousands or millions of DNA particles to make DNA samples large enough to analyze. This technique is used most commonly in diagnostics for hereditary and infectious diseases, forensic research, and paternal testing. The process involves the repeated heating and cooling of the DNA environment to have a successful cloning reaction.

Our first task of the prototyping phase for Nexogen’s PCR machine was to reproduce all the functionality of their existing PCR equipment. This PCR machine was running on an inexpensive processor incapable of triggering, timing, or acquiring certain signals. The most critical feature required on the new prototype was the ability to flash a high-intensity LED synchronized with an industrial camera used for DNA image capture. Since the duration and latency of the LED pulse and the duration of the camera sensor imaging were unknown, tests had to be carried out with varying degrees of delay between the trigger pulses. Triggering was carried out on the field-programmable gate arrays (FPGAs) directly to ensure tight synchronization and minimal jitter between the pulses of the LED and the camera. Therefore, the PCR machine required deterministic hardware-based timing.

The final implementation included triggering settings issued from the real-time operating system (RTOS) to the FPGA. When the values were detected, the signals were composed by the FPGA and multiple triggers were generated with the appropriate delay. The overall per-cycle resolution of the FPGA timing was 25 nanoseconds.

The PCR machine for Nexogen required various process management devices including:

  • Stepper motors
  • Thermoelectric cooling devices
  • Resistance temperature detectors (RTDs)
  • High-intensity LEDs
  • Galvanometers
  • Laser diodes
  • Fans
  • Peltiers
  • Heat sinks
  • Heaters
  • Safety interlock sensors
  • Touch-screen monitors

Our solution included all input and output (I/O) functionality and interaction within the first three days. The control algorithms were functional within the first ten days. The HMI, the enclosure, and the rest of the system integration took place over the following week. All of this was possible for both Cyth and Nexogen because of the CircaflexTM Developer Suite, our off-the-shelf control system product based on NI Single-Board RIO and NI LabVIEW software. The Circaflex Developer Suite includes a daughterboard built on an NI Single-Board RIO device with hardware features on the daughterboard like fuse protection, LED indication for all I/O, and immediate screw terminal and customizable connectivity and interaction with customer I/O. In addition to the hardware features on Circaflex, the control platform includes pre-developed signal conditioning and software code for the RTOS, FPGA, and HMI. This feature helps developers stay on schedule and reduce risk in their projects with a customizable commercial off-the-shelf device.

The additional and unexpected benefit that Nexogen experienced from working with us was the rapid completion of their product after only a couple of weeks. “With Circaflex, it took only 15 days for us to achieve a working system that included all our necessary, customized sensors,” said Dalibor Hodko, CEO of Nexogen. “Building a control board with custom products would have taken five times as long and cost at least five times as much as what we created with Circaflex.”

Cyth System’s off-the-shelf features included with the Circaflex design helped Nexogen rapidly develop their product. Product developers, from university researchers and chemists to electrical and biomedical engineers, can use Circaflex to deliver critical, high-speed control without the need for costly and time-consuming custom FPGA programming.

© 2012 Cyth Systems, Inc. All rights reserved. Product and company names are trademarks or trade names of their respective companies.

Author Information:
Candice Garcia
Cyth Systems

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