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🧪 Automated Bioreactor — SystemUnite4

Automated Bioreactor & Incubation Controller

Platform Language Protocol License

📑 Table of Contents

🔬 Overview

SystemUnite4 is an embedded master controller engineered to automate microbial incubation and bioprocess regulation. It combines dual-zone digital temperature monitoring, independently-driven heating elements, dual-channel aeration control, Bluetooth telemetry, and a local LCD interface into a single closed-loop bioreactor/incubator controller.

The system is built around an Arduino Mega 2560, communicates with an Android control app over a Bluetooth serial link (HC‑05), and displays live process data on a 16×2 I2C LCD — so the reactor can be monitored and operated even without the phone connected.

✨ Key Features

  • Dual-Zone Thermal Monitoring — two DS18B20 digital sensors on a shared OneWire bus (Pin 9) give independent upper-zone (T1) and lower-zone (T2) temperature readings.
  • Independent Heater Control — the upper and lower heating elements are switched separately, each compared against its own zone's reading.
  • Dual Aeration Channels — two independently-addressable air-pump relays (AIR1 / AIR2) for oxygenation or mixing during fermentation cycles.
  • Bluetooth Telemetry (UART) — a serial command protocol over Serial1 accepts remote START / STOP / TEMP / TIME / AIR commands and streams live temperature data back to the app.
  • Local HMI (I2C LCD) — a 16×2 display (0x27) shows both temperatures, the setpoint, and the countdown timer without needing the phone.
  • Status LEDs — dedicated indicators for run state, stop state, aeration, and each heater zone give an at-a-glance hardware status even from across the room.
  • Companion Android App — a KivyMD-based Bluetooth control app (APP) with live gauges, parameter entry, and start/stop controls.

🏗️ System Architecture

flowchart LR
    subgraph UI["User Interface"]
        APP["Android App\n(Bluetooth Terminal)"]
    end

    subgraph COMM["Wireless Link"]
        HC05["HC-05 Bluetooth Module\n(Serial1, 9600 baud)"]
    end

    subgraph MCU["Arduino Mega 2560 — Main Controller"]
        PARSE["Command Parser"]
        CTRL["Control Logic\n(Heater / Aeration / Timer)"]
        LCD["LCD Interface (I2C 0x27)"]
    end

    subgraph SENSE["Sensing"]
        DS1["DS18B20 #1 (T1, Upper)"]
        DS2["DS18B20 #2 (T2, Lower)"]
    end

    subgraph ACT["Actuation"]
        H1["Upper Heater Relay\n(Pin 44)"]
        H2["Bottom Heater Relay\n(Pin 45)"]
        A1["Air Pump #1 Relay\n(Pin 42)"]
        A2["Air Pump #2 Relay\n(Pin 43)"]
    end

    APP <-->|Bluetooth SPP| HC05
    HC05 <-->|UART| PARSE
    PARSE --> CTRL
    DS1 --> CTRL
    DS2 --> CTRL
    CTRL --> H1
    CTRL --> H2
    CTRL --> A1
    CTRL --> A2
    CTRL --> LCD
    CTRL -->|T1 / T2 stream| PARSE

    style MCU fill:#203a43,stroke:#4ec9f5,color:#fff
    style SENSE fill:#2c5364,stroke:#81c784,color:#fff
    style ACT fill:#2c5364,stroke:#ffb74d,color:#fff
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For a deeper, command-level walkthrough of the decision logic, see ARCHITECTURE.md.

🔌 Hardware Pinout & Wiring Configuration

Component / Subsystem Pin Name Arduino Pin Description
DS18B20 Sensors ONE_WIRE_BUS Pin 9 Shared digital temperature data bus (2 sensors)
Blue Status LED startLed Pin 24 Operational state indicator
Red Status LED stopeLed Pin 25 Emergency / standby indicator
Air Status LED airGeneratorLed Pin 26 Aeration active indicator
Heater 1 Indicator heaterLed1 Pin 27 Upper heater status LED
Heater 2 Indicator heaterLed2 Pin 28 Bottom heater status LED
Aeration Relay 1 airGenerator1 Pin 42 Primary air injection relay
Aeration Relay 2 airGenerator2 Pin 43 Secondary air injection relay
Upper Heater Relay upperHeater Pin 44 Upper heating element actuator
Bottom Heater Relay bottomHeater Pin 45 Lower heating element actuator
I2C LCD Module SDA / SCL Dedicated I2C System status & display (0x27)
Bluetooth Module Serial1 (RX1/TX1) Hardware UART Remote telemetry interface, 9600 baud

Full electrical specs — sensor accuracy, pull-up values, relay isolation, power budget — are in HARDWARE.md.

🎛️ Control Logic

Each zone runs an independent on/off threshold controller: a heater is driven while its own sensor reads below the shared desiredTemp setpoint, for as long as the countdown timer and START state remain active.

stateDiagram-v2
    [*] --> Idle: Boot / STOP received
    Idle --> Running: START received
    Running --> Idle: STOP received\n(all outputs forced OFF)
    Running --> Running: Read T1 / T2 every 1s
    Running --> Idle: Countdown reaches 0\n(auto safety shutoff)

    state Running {
        [*] --> CheckZones
        CheckZones --> UpperHeaterON: T1 < desiredTemp
        CheckZones --> UpperHeaterOFF: T1 >= desiredTemp
        CheckZones --> LowerHeaterON: T2 < desiredTemp
        CheckZones --> LowerHeaterOFF: T2 >= desiredTemp
    }
Loading
  • Setpoint (desiredTemp) and run duration (countdownTime) are both configurable at runtime over Bluetooth (TEMP:<val>, TIME:<sec>), with no reflash required.
  • STOP and timer-expiry both perform a full safety shutoff — heaters, aeration, and their status LEDs are all forced off in the same code path.
  • The loop samples and updates once per second; command handling happens on every pass of loop(), so START/STOP are responsive even mid-cycle.

📡 Wireless Bluetooth Serial Protocol (UART)

Command Example Action Taken
START START Initiates the closed-loop process & timer
STOP STOP Immediately cuts off all heaters and air pumps
TEMP:<val> TEMP:37 Sets the desired thermal setpoint (37 °C)
TIME:<sec> TIME:1800 Sets the process run timer (1800 s)
AIR1:ON / AIR1:OFF AIR1:ON Toggles the primary aeration pump
AIR2:ON / AIR2:OFF AIR2:ON Toggles the secondary aeration pump

The controller streams T1:<value> and T2:<value> lines back over the same link once per second while the process is running, which the app parses to drive its live gauges.

📱 Companion Mobile App

The APP file is a KivyMD (Python) Android application that pairs with the HC‑05 module over classic Bluetooth SPP and provides:

  • Live circular gauges for T1 and T2, color-coded by temperature band (Cold / Optimal / Warm / Hot)
  • Text fields to set the target temperature and run timer, transmitted as TEMP: / TIME: commands
  • Toggle controls for both aeration channels
  • Start / Stop buttons that mirror the firmware's START / STOP commands
  • A live hardware-status card showing connection state (LIVE / SCAN / OFF)

It uses Android's native Bluetooth API via pyjnius, so it must be packaged with a tool such as Buildozer into an APK to run on-device — it will not run as a plain desktop Python script.

🛠️ Installation & Dependencies

Firmware (Arduino Mega 2560)

  1. Install the following libraries via the Arduino Library Manager:
    • OneWire (Paul Stoffregen)
    • DallasTemperature (Miles Burton)
    • LiquidCrystal_I2C (Frank de Brabander)
  2. Wire the hardware according to the pinout table above.
  3. Connect your Arduino Mega 2560, select the correct COM port, and upload SystemUnite4.ino.

Companion App

  1. Requires kivy, kivymd, and pyjnius (Android-only Bluetooth bridge).
  2. Package with Buildozer for Android; the native Bluetooth calls will not run on desktop Python.
  3. Pair your phone with the HC‑05/HC‑06 module beforehand — the app looks for a bonded device named HC-05, HC-06, or SystemUnite.

🗂️ Repository Structure

File Role
SystemUnite4.ino Main firmware — sensors, heater/aeration control, LCD, Bluetooth
APP KivyMD Android companion app (Bluetooth control + live gauges)
ARCHITECTURE.md Command-level logic flowchart and control-loop diagrams
HARDWARE.md Full electrical specification, pinout, and wiring reference
CONTRIBUTING.md Contribution guidelines
LICENCE Project license
docs/ Diagrams and images used in this README

🚧 Current Status & Roadmap

This is an active academic/lab project, not a finished production controller. Documented honestly for anyone building on it:

  • Timing model: the main loop uses a blocking delay(1000) for its once-per-second update, so Bluetooth commands are only read once per second rather than continuously. A millis()-based non-blocking loop (as recommended in CONTRIBUTING.md) is a natural next step.
  • Threshold control, not hysteresis: heaters switch at a single desiredTemp boundary rather than a low/high hysteresis band, so relay chatter near the setpoint is possible — a hysteresis band would reduce relay wear.
  • No persistence: desiredTemp and countdownTime reset to their defaults on every reboot; there is no EEPROM/NVS save of the last configuration.
  • Stirring/agitator relay reserved, not wired: HARDWARE.md and the architecture diagram reference an optional stirring motor channel that is not yet implemented in SystemUnite4.ino.
  • No watchdog or sensor-fault handling yet: unlike the hysteresis/safety layers in related ESP32-based incubator projects, this controller does not currently detect a disconnected DS18B20 or recover from a stuck relay automatically.

None of this blocks using the system as-is for supervised lab runs — it's simply the gap between the current firmware and a fully autonomous, unattended controller.

👥 Academic & Engineering Credits

Project Leadership & Supervision

  • Prof. Dr. Salah Badr — Principal Supervisor, Laboratory Host & Primary Sponsor
  • Dr. Ragab Qasem — Main Co-Supervisor (Scientific & Engineering Lead)
  • Dr. Omar — Co-Supervisor & Academic Mentor
  • Mr. Mostafa Fathy — Lead Embedded Developer & Project Creator

Dr. Ragab Qasem is the main supervisor responsible for all scientific and engineering aspects of the project.

🙏 Acknowledgments

  • Prof. Dr. Salah Badr — for direct supervision, funding the project, providing full access to his specialized research laboratory, and empowering the execution of this work.
  • Dr. Ragab Qasem — for hands-on technical guidance, invaluable expertise, and dedication throughout every stage; his patience, problem-solving support, and scientific mentorship were foundational to this implementation.
  • Dr. Omar — for the insightful advice and guidance that were the primary catalyst for initiating this project, and the continuous motivation that drove it to completion.

🤝 Contributing

See CONTRIBUTING.md for how to report bugs, suggest new modules (e.g. pH or dissolved-oxygen sensors), and submit pull requests.

📄 License

See the LICENCE file in this repository.

About

An Arduino Mega automation system for a closed batch fermenter with real-time temperature monitoring, heating control, aeration management, sensor integration, and process automation. Designed for microbiology, biotechnology, and embedded systems projects.

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arduinoarduino-megaautomationautomationscppembedded-systemsembedded-systems-and-iotembedded-systems-autonomous-systemsembedded-systems-programmingfermentationfermentation-chamberfermentation-monitoringiotiot-applicationtemperature-controltemperature-control-appptemperature-control-systemtemperature-controller

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