Software

Introduction

Through the lens of synthetic biology, our team delved into the realm of spectrophotometry, a pivotal tool that enables the quantitative analysis of molecules and their interactions. While engaged in our research, we encountered several challenges with traditional spectrophotometers: complex user interfaces, compatibility issues with newer hardware, and laborious data collection and analysis processes. It was these very hurdles that sparked our innovative journey towards Espec - a software designed to bridge the gap between user needs and the functionality of second-generation spectrophotometer hardware. Espec eliminates the complexity of device interaction by providing an intuitive user interface, allowing for straightforward trendline plotting, RGB LED control, and enabling direct activation of blank tests.

Not just another software, Espec is crafted with the iGEM spirit, intending to make synthetic biology more accessible and efficient. At its core, it provides:

• Intuitive User Interface: Facilitating researchers to focus on scientific exploration rather than tool manipulation.
• Trendline Plotting: Empowering users with the capability to input absorbance values and concentrations for effortless data interpretation.
• RGB LED Control: Delivering real-time feedback through a vivid display and facilitating various experimental conditions.
• Blank Test Activation: Enhancing workflow efficiency by enabling direct controls from the software interface.

Utilizing the Ionic framework and ensuring robust communication through ESP32, Espec promises seamless and reliable interactions between users and the hardware.

Espec in Action: A Detailed Walkthrough

Exploring deeper into the functionality of Espec, we discover an orchestrated workflow that ensures precision and user-friendliness:

• Initiating Espec: A smooth commencement as users activate the Espec application.
• Engaging with Arduino:
  • Inputting the IP address of the ESP32.
  • Ensuring IP validation and providing options to reconnect in case of discrepancies.
• LED Customization: Offering a spectrum choice of red, green, or blue LEDs, tailored to user preferences.
• Data Harvesting from Arduino:
  • Scheduled data retrieval every 5 seconds.
  • Displaying illumination, blank, test, and computational values in an intelligible format.
• Calibration Curve Insights:
  • A dynamic platform allowing data manipulation - addition, preservation, or deletion.
  • Providing options to cleanse all data or construct a trendline for enhanced clarity.
• Trendline Data Exposition:
  • Displaying predicted concentrations, trendline equations, and R-squared values for analytical clarity.

Espec's User Interface: A Synthesis of Form and Function

Emphasizing both aesthetics and utility, Espec's user interface is a manifestation of its capabilities, establishing a seamless bridge between the user and the underlying algorithms. Espec prioritizes intuitive navigation along with a sleek design, highlighted in the following screenshots:

Screenshot 1: The Dashboard
Here lies the heart of Espec. The dashboard is designed with the user's workflow in mind. From connecting to Arduino, selecting LED colors, to viewing real-time data - everything is a click away. Clear icons, legible fonts, and an organized layout ensure even first-time users feel at home.

Screenshot 2: Data Visualization and Trendline Analysis
Diving into the analytical aspect, this screen is where raw data transforms into insightful graphs and trendlines. With options to customize, save, or reset, users have complete control over their data representation.

Espec's user interface is not just about aesthetics; it's about making spectrophotometry an engaging, efficient, and enlightening experience.

Prospects & Challenges

Espec finds its utility beyond laboratories, marking its presence in various domains that require optical measurements, such as food safety, environmental monitoring, and clinical diagnostics. Within our laboratory settings, Espec has shown preliminary potential in decolorization experiments and in employing laccase with ABTS to measure decolorization efficiency. While the software provides a platform to monitor and analyze absorbance values during enzymatic reactions, it's pivotal to note that both the findings and the software's application are in the nascent stages, necessitating further validations and optimizations.

We recognize that Espec has its limitations, such as its primary optimization for second-generation hardware and the necessity to explore a broader spectrum of device compatibilities. Yet, inspired by the iGEM spirit of continuous innovation, our future directions include enhancing Espec's features based on user feedback and expanding its compatibility to a diverse range of laboratory instruments, thereby amplifying its applicability.

Documentation

This manual provides detailed information on using the Espec software. In addition, both the Ionic version and the web version of the software can be downloaded and used on GitHub.

Explore More on GitHub For comprehensive insights and further information about our project, visit our GitHub page:2023.igem-csmu-taiwan Repository . This repository houses all the resources, updates, and collaborative opportunities associated with our iGEM Hardware & Software Open-Source Project. Your exploration and contributions are highly appreciated!

Conclusion: Embarking on a Journey with Espec

Espec, inspired and driven by the iGEM ethos, endeavors to redefine the boundaries of tools available to synthetic biology researchers. By simplifying spectrophotometry, making it more intuitive, and ensuring compatibility with modern hardware, we envision paving the way for groundbreaking discoveries in synthetic biology. We cordially invite the iGEM community to join us on this journey, test Espec, and be a part of this transformative endeavor. Together, let's enhance the accessibility, efficiency, and impact of scientific research!