This repository contains a graphical user interface, arduino libraries, and modules that are used within PhageBox. Below are instructions for using this code base, as well as information for initiating the GUI.

For building the phagebox, please review the build manual for a step-by-step build process.

Please see the GUI diagram for more information on what the GUI looks like once opened.

General Usage:

usage: phagebox_app.py [-h] -s SERIAL_PORT [-m SLOPE] [-b INTERCEPT] [-v]

optional arguments:
  -h, --help            show this help message and exit
  -s SERIAL_PORT, --serial_port SERIAL_PORT
                        Specify the serial port
  -m SLOPE, --slope SLOPE
                        Slope of (Chip Temp vs Peltier Temp) [Default 1.2]
  -b INTERCEPT, --intercept INTERCEPT
                        y-intercept (Chip Temp vs Peltier Temp) [Default -2]
  -v, --verbose         prints output figures and debug info

Example (Mac):

python phagebox_app.py -s /dev/tty.usbserial-1430

Example (Windows):

python phagebox_app.py -s COM4

To use this library, drag the entire contents of src/phagebox_embedded/ into your local arduino libary and import. More detailed instructions can be found in the arduino documentation.

This example uses an Arduino sketch to import the PhageBox library and initialize the embedded software. This sketch is also available here: PhageBox/arduino/phagebox_controller/phagebox_controller.ino

#include <PhageBox.h>

void setup()
{
    Serial.begin(9600);
    init_phagebox();
}

void loop()
{
    start_phagebox();
}

Once installed, you can send commands through Serial/UART for controlling backlight, magnetic module and temperature modules:

1. Heater 1 for 32 PCR cycles. Cycles: 15 seconds at 90C, 20 seconds at 50C, and 60 seconds at 72C.

<H,1,32,15,90,20,50,60,72>

2. Heater 2 for 32 PCR cycles. Cycles: 15 seconds at 90C, 20 seconds at 50C, and 60 seconds at 72C.

<H,2,32,15,90,20,50,60,72>

3. Toggle the LED

<B,0,1>

4. Toggle the MAGNET

<B,1,0>

5. Toggle both the MAGNET and LED

<B,1,1>