Features

Introduction

Welcome to the hardware for 2019 iGEM team GENAS_China. Our team aims at creating a modular way to detect the concentration of certain small molecules in the human body as disease indicators. The hardware appliance is to be used in couple with our detection liquid based on a genetically modified strand of the E. Coli O157. For a detailed description on our project, check us out on the iGEM website (still under construction) or the CCiC compliant preview website.

Although our aim is that the user can directly see the danger level of the molecule (as indicated by the liquid turning into different colors), the hardware is meant to quanitfy the concentration level as well as complementing the previous method when determing the danger of a certain molecule requires more precision than the previous method can offer.

The intuition behind the hardware is that the blue lights emitted from the bottom of the box pass through the sample liquid on a piece of translucent paper and excite the flourescent protein in the sample. The light is then received by a light intensity sensor, on which there is an ochre-colored filter, so that the level of excited flourescent light can be measured. The light is also received by an unfiltered color sensor, so that the color of the light can be measured. The measurements are then correlated with a pre-built math model to determine the concentration and mix formula of expressed flourescent protein, which is then used to find out the concentration level of the certain particle.

The current protoype is based on a Raspberry 3 Pi B+, but can be produced on a Pi Zero too, which cuts the cost of manufacturing to less than $30.

Startup script checks if all interfaces can be instantiated and print out the currently connected Wi-Fi network and its IP address for easy SSH for the developer. Should the user decide that he/she wants to enter the user mode, which outputs the measured concnetraion based on sample, he/she needs to push the button after the first LCD message.

List of sensors currently installed:

• TCS34725 color (RGB) sensor with inaccurate light intensity function
• DS18B20 temperature sensor
• TSL2561 light intensity sensor

Design diagrams

1 2 3

User mode (model still under development)

To enter user mode

Push the button when the LCD displays the Wi-Fi information. From there you can use the appliance to get concentration data from samples based on previous models (which are to be built).

To use user mode

Put in your sample when the screen prompts you to. After you put in the sample, push the button and the machine will start analyzing it. When it is done analyzing, the measured concentration level will be printed out on the LCD screen and one of the LEDs (green, yellow, red) will light up to indicate the status of your sample (good, worse, bad). Then when you are done viewing the results of this sample, push the button again and start over from the beginning of this paragraph.

Startup sequence

To run the startup script, type sudo python practice.py in the terminal when in this directory. The startup script should detect most of the connection problems. Should there be no connection problems, events that would happen when you plug in are as follows:

• LCD screen prints out "LCD Success".
• LEDs show a light chasing sequence, then all flash three times.
• LCD screen prints out "All OK" on first line, "Lux=...,T=..." on second line.
• As soon as the Pi is connected to the network, LCD screen prints Wi-Fi network name on first line, local IP address on second line (which is the IP address you use to connect to the Pi).

Allow 30 seconds before the Pi starts the startup sequence above. Should the startup not abide to the sequence above, the LCD should print out the error (if the LCD is working in the first place). Refer to the "Errors" section below for more information.

Setting up the hardware and software

1. Use Etcher to flash Raspbian image to the Pi.

2. Add an empty file named ssh to the boot partition. This enables the ssh daemon when it boots.

3. Edit these files on the OS partition:

• Edit /etc/hostname and /etc/hosts to change “raspberrypi” to a unique host name, like smart-detector-pi.
• Edit /etc/wpa_supplicant/wpa_supplicant.conf to add your WiFi authentication (updating "country" if appropriate):

country=us
update_config=1
ctrl_interface=/var/run/wpa_supplicant

network={
 scan_ssid=1
 ssid="your WiFi name (SSID)"
 psk="your WiFi password"
}

4. Use an IP scanner (such as the "Advanced IP Scanner" for Windows) to scan the network of the Pi. Once you find a device with the special name that you set in step 3, copy down its IP Address. Then use PuTTY to connect to the Pi via SSH by changing the hostname or IP address field to the one that you found.

5. Run the following commands to start the setup script.

wget https://raw.githubusercontent.com/longyuxi/2019-genas-china-smart-device/master/setup.sh
chmod +x ./setup.sh
sudo ./setup.sh

6. Run crontab -e and append the line @reboot sudo python /home/pi/2019-genas-china-smart-device/practice.py & to run the script at startup.

To view the wiring diagram

Download Fritzing to open the .fzz file. You possibly need to download the Fritzing parts file for TCS34725.

To log data

Currently, in order to log the data, you have to SSH into the Pi and run a Python script. This will be improved in the future.

1. When in the 2019-genas-china-smart-device directory, run sudo python record_data.py. Make sure the box is empty.
2. Leave the lid closed until the script prompts you to insert your sample.
3. Open the lid.
4. Put in/replace the sample.
5. Key in the flow cytometry-determined flourescent value and press ENTER.
6. Repeat from step 3. When you are done, hit CTRL + C on your keyboard to exit the program.

The file is automatically saved every time you press ENTER, so no worries if the power goes out.

Potential errors and error messages

1. There is no output on LCD: There is probably a connection problem between the Pi and the LCD. Refer to the wiring diagram to correct the connection. If there is no problem in connection, there might be a problem auto-executing the script. Make sure you have followed all the steps in the setup section above.
2. TCS34725 FAIL, LED FAIL, DS18B20 FAIL, TSL2561 FAIL or Emitter FAIL: Refer to the wiring diagram to correct the wiring.
3. Wi-Fi not connected: Make sure you are in range of the Wi-Fi adapter. The wireless adapter on the Raspberry Pi might be less powerful than your computer or phone's Wi-Fi adapter.