What is NOX Kit

NOX Kit is a general biology experiment environmental detection hardware kit that provides temperature control, temperature, and bioluminescence monitoring functions.

Animation of NOX Kit Project

In this project, our bioamplifiers can amplify trace analytes and convert them into bioluminescence. Currently, expensive fluorescence microscopes are often required to detect bioluminescence reactions, which makes large-scale measurements difficult. To enable low-cost and high-throughput detection, we designed the NOX Kit to address this need.

NOX Kit has the following features (see the Feature Description section for details):

• Modular Design: Extensible configuration, add/remove modules by needs
• Multiple Working Modules: Works standalone or in array for high-throughput
• User-friendly Interface: Simple clicks to collect and visualize data in real time
• Reproducible Low-Cost Design: Core board costs less than $1 (5 RMB). Streamlined for statble reproduction and mass production.

So for general users, NOX Kit is simple and easy to use - just connect and collect/visualize data. For developers, NOX Kit is low-cost and extensible - build upon it to create more low-cost, high-throughput biosensors.

Development Story

During the development of NOX Kit, we investigated the needs and experiences of biological experiments, and went through multiple iterations of prototypes and development to arrive at the final NOX Kit.

Developing the Prototype Shell Design through team discussion

Through exchanges with the experiments team, we made multiple revisions to the detector prototypes, solving many practical problems including but not limited to:

• Reducing reagent waste and position-dependent effects by constraining reaction chamber volume
• Improving signal sensitivity within the detection range by iterating the detection elements
• Improving user experience through shell design and software optimization
• …

Through this process, we accumulated much design experience:

• Hardware design through modeling/simulation combined with experimental validation
• Economic selection of equivalent hardware to ensure performance at lower cost
• How to enable better team communication and collaboration
• …

This ultimately led to the modular NOX Kit we have today.

A Single Detector Prototype in Standalone Mode

Model Validation

To validate that our model could achieve the detection goals during design, we collaborated with the modeling team to design the reaction chamber: By using COMSOL Multiphysics to model the diffusion and fluorescence of the analyte introduced into the reaction chamber, we evaluated the effects of different chamber shapes on the fluorescence emission.

In this model, to simplify the process, the analyte diffusion was modeled as a fluid with streamlines and flux tracking the diffusion and distribution over time. The light intensity on the photoresistor was then evaluated at specific time points based on the analyte distribution, assessing the detector design.

Simulation results via COMSOL

More details on the modeling validation process can be found in the Modeling section.

By modeling the underlying phenomena, we could optimize the chamber geometry, heating, and optical sensing before physical implementation.

Feature Description

Modular Design

To accommodate different workflow needs and detection sensitivity ranges, different modules can be added/removed:

• Core Board

  The core board uses an STC8G1K08A MCU, photoresistor and thermistor for bioluminescence and temperature sensing.

• Heating Module

  Choices include PTC heating modules (5V 1A 1W) or semiconductor temperature control modules (5V 1A 1W).

• Power Module

  Can be powered by 3.7V lithium batteries, 5V DC or 5V USB.

• …

This project can also serve as a base kit, with more modules added through extensions in the future. It can be ported to more biosensing applications.

Multiple Working Modes

NOX Kit can work in different modes:

• Single Detector Mode

  NOX Kit can communicate directly with the PC over serial, serving as a standalone detector. For example:

  

  A gas phase trace element detector using NOX Kit with a heating module

  In the above example, the air is pumped into the reaction chamber by a fan. Bioluminescence produced by the bioamplifier is detected and the signal sent to the PC.

• High-Throughput Array Mode

  

  NOX Kits connected in an array via I²C bus

  NOX Kits can connect to a host over I2C bus, allowing one host to control multiple detectors as an array for high-throughput detection.

User-Friendly Interface

For general users, NOX Kit provides a data collection program for single detector mode:

NOX Monitor, the GUI program to recording the data

Users can collect and visualize data through simple interactions.

For developers, NOX Kit provides a Python interface class for easy integration.

Reproducible Low-Cost Design

Common iGEM projects are often built on generic dev boards (Arduino, Raspberry Pi), which are often overkill and costly, making large scale production difficult.

To address this, NOX Kit uses low-cost and readily available components. Thanks to the bioamplification of NOX, trace analytes can be easily amplified to generate a SNR of ~1400 under a fluorescence microscope. This allows the use of more affordable detection elements while achieving results comparable to high-precision instruments.

What's more, in order to reduce the work required for users to construct the NOX Kit, we have also encapsulated the circuitry into a PCB. This allows users to simply download the PCB files, consult local retailers that provide relevant services, and obtain a sleek, elegant NOX Kit PCB for detection and development through simple soldering work.

3D Model of NOX Kit PCB

The core board costs under $0.8 to manufacture (see Bill of Materials).

Future Improvements

NOX Kit allows anyone to use our detector affordably.

The fully-featured and extensible hardware can also be iterated on in the future:

• Add more expansion modules: Like a display module for standalone data visualization without a PC
• Streamline the reaction chamber for a more compact form factor and portability
• Package NOX Kit and define standard interfaces for commercialization, providing more affordable and easy-to-use detection tools for biological experiments. Building on the open-source foundation while generating revenue through technical support and education.

Appendix: Technical Details

User Manual

Hardware User Manual

NOX Monitor

Using python to run main.py via python3 main.py under pyserial folder. The left panel is the control panel. Select the connected NOX Kit serial port, click Start to begin data collection, Stop to end it, and Save to store collected data locally. The right panel visualizes the collected data.

Biosafety

In addition, our hardware adhered to a predetermined and standard operating method for the workflow. To prevent residue after use, decontaminate the device by 30 min UV irradiation and alcohol wiping.

This not only reduced the likelihood of any potential safety issues occurring, but it also lowered the risk of any engineered bacteria escaping into the environment. This location has other details pertaining to the Hardware that may be found.

For detailed biosafety, please see Safety section.

Developer Manual

Single Detector Mode

Communicate via UART protocol. Send commands to the serial port to get corresponding results:

UART Command Table

For single detector data collection, NOX Kit provides the NOX Monitor GUI for general users and the Python NOX library for developers.

Multi-Detector Array

Connect to host via I2C bus. When compiling firmware, set the I2C address of each detector. Then access data by specifying the address and register:

I²C Data Address

Connecting multiple detectors via the host allows high-throughput array detection.

Python NOX Usage

NOX Kit provides the following Python class for easy integration:

from nox import nox

board = nox(port)    # <= the port of nox kit 
board.temp()         # => read temperture
board.photo()        # => read photoresister

Assembly Guide

1. Prepare components

   All project files are open-source, 3D part models are in 3dmodel (SolidWorks).

   See Bill of Materials for core board components.

   For the detection elements, the pairing resistor is selected as: $R_{\mathrm{pair}} \approx \sqrt{R_{\mathrm{sensor\ work\ point}}}$, where $R_{\mathrm{pair}}$ is the pairing resistor and $R_{\mathrm{sensor\ work\ point}}$ is the sensor resistance at its operation point.

2. Solder circuit board

   The streamlined core board uses few components and is easy to reproduce:

   

3. Assemble parts

4. Flash firmware

   See the Rakefile script in source code for operations.

Bill of Materials

Core Board BOM Table (1 CNY = 0.14 USD, 2023/10/8)