Team:Washington/Hardware
Overview
This year, the UW iGEM team has created the Chromastat: an affordable, modular, and autonomous turbidostat + color detector. Our hardware project began with a review of the UW iGEM 2016’s designs and concepts. The general idea of a control system had been suggested, but not yet implemented. Because the project required an improvement of the pump, a set of sensors, and a system of responsive real-time control, we decided to begin by dividing the task into the following categories and domains of responsibility:
| Task | Responsibility |
|---|---|
| Sensors | Choosing appropriate sensor hardware and designing ways to attach them. |
| Pumps and Fluids | Improvement of the syringe pump design, with focus on accuracy. |
| Tank | Research methods of delivering inducer and media fluids into the bioreactor beaker and removing waste products. |
| Integration | Design response and control software, and create a user-friendly interface that runs on a Raspberry Pi. |
The parts list for our project can be found here: https://static.igem.org/mediawiki/2017/f/f2/T--Washington--PartsList.xlsx
Raspberry Pi and Control
Figure: Raspberry Pi
The Raspberry Pi is an inexpensive, credit card-sized computer. It runs on a variant of the open-source operating system, Linux. This means that it allows the use of any major programming language. A Raspberry Pi can be operated by connecting a keyboard and monitor, or by accessing it remotely with a PC or major smart phone. This ease of access allowed us to choose between a broad range of approaches for software control. We chose the popular Java Swing user interface platform as our way for the user to configure and operate the system.
The general solution follows from connecting the Raspberry Pi’s low power logic system (“GPIO” pins) to a simple integrated circuit capable of turning device components on and off as required. Through our easy-to-use Java software, a user can control all of these components without the need for any special technical knowledge.
The Raspberry Pi itself is a low-voltage logic system that cannot provide much power. In our device, the Pi is connected to a circuit board that allows this low-voltage logic to control more power-intensive devices such as a heater, bubbler, and magnetic stirrer. Power to these devices comes from a low-cost PC power supply of the kind used in inexpensive desktop computers.
Sensors:
- The TSL2560 light sensor that we used for turbidity is designed for sensing changing light conditions. For example, it is suited for use in a cell phone to adjust screen brightness when you go inside.
- The Si7021 temperature/humidity sensor was designed for heating and humidity controls in HVAC systems, and is very tolerant to changes in both.
- The TCS34715 color sensor is a high-accuracy RGB sensor that was designed for calibrating digital displays and sensing color in medical diagnostic equipment. It works very similarly to our lux sensor, but has special filters that allow it to sense colors.
- Both the color and light sensors are calibrated in our software to approximate the human eye response to changes in color and brightness, so readings will not only be precise, but will be intuitive when compared with human observation.
Documentation for the sensors: https://github.com/uwigem/uwigem2017/tree/master/docs/specSheets
Syringe Pump
Our syringe pump was custom designed from the ground up, is open source and 3D printable, and is cost effective. Industrial syringe pumps with the feature set that we provide (high accuracy, programmability, and automatic refilling) cost around $1000, whereas our creation only costs around $80 total to create and assemble, provided that a 3D printer is available. Because the accuracy of our pump comes from the linear actuator (stepper motor and drive assembly), the accuracy varies by syringe size. This allows the user to choose between a larger, slightly less accurate syringe or a smaller more accurate one. Software calibration makes it easy for the software to adjust to nearly any standard syringe size. Using a standard 3mL syringe, our pump is accurate to +/- .01 mL for any given dispense action.
To read about our Syringe Pump design process, please check out our Design page.
Find the STEP files for our open source syringe pump here: Syringe Pump STEP files
Oxygen Input
To aerate our culture we chose an aquarium pump, the Stellar Air Pump S-30, which retails for around $15. We modified the power plug to be controllable by solid state relay from the Raspberry Pi. We placed a 0.1μm filter in-line between the pump and culture to reduce contamination.
Spinner
We wanted to ensure that the system would not only be aerated, but well-mixed. The assumption of being well-mixed is built into our sensing apparatus, so it was important to use a system that could keep the culture mixed thoroughly without exposing it to contaminants.
This is achieved using a magnetic spinner to suspend the culture. We used a magnetic spin bar inside the culture and controlled that from the underside with a custom printed platform using inexpensive disc magnets and a lightweight motor.
The primary difficulty we encountered when assembling a low-cost magnetic stirrer was that most inexpensive electric motors revolve too quickly to effectively stir the solution. . A motor that spins at 3,000 RPM, for instance, can be obtained for about $5. We reduced the motor by controlling its activation with a transistor and turning it on and off rapidly via software on the Pi. This implements pulse width modulation.
Find the STEP files for our open source magnet spinner attachment here: 3D Printed Spin Vane Stirrer
Enclosure
The enclosure is a structure created from aluminum metal and acrylic (Plexiglas) windows. It houses the three syringe pumps, culture tube, magnet spinner, aerator, Raspberry Pi, sensors, and custom circuit board.
Aluminum extrusion for the frame was purchased from a hardware store at a low price, and Plexiglas sheets were purchased from a scrap heap. We were donated some aluminum metal from a drylab member’s old robotics team, Punahou School Robotics.
The main goal of the enclosure is to be modular. The front and top panel can open to immediately give us access to the culture tube and the electronics in case there is an error. Sitting on a top shelf is the Raspberry Pi and circuit board, which can be slid on and off with ease. On a secondary shelf is a 3d printed mount for the culture tube to sit in. This shelf also will store the inducers and media required for the culture. On the bottom shelf is the power supply, the magnet spinner, and the aerator. Finally, on the outside side panel are the three syringe pumps
Find the STEP Files for our open source Enclosure here: Enclosure STEP Files
