Cellerator - biological computer

To keep prices low.  Bench tools are controlled via an Arduino Uno via I2C protocol. The Arduino uses a blank PCB board propagated with an RJ11 jack,  XHP-JST, and other electrical components.   The RJ11 jack is connected to the IC2 Pins located at A4 and A5.  XHP-JST connectors are used to make connections with external sensors or inputs.  Lastly, the PCB can accommodate other electrical components: LEDs, Resistors, ICs and the like.

Hand

The drivetrain positions the hand over the hand tool. The hand and hand tool are connected via magnets and by the geometry of the hand tool insert. This aligns the pogo pins to the hand tool pads. The drivetrain moves in the X-Axis, sliding the Hand tool off of the tool shelf.

• (2x) RJ45 Breakout Board - one for the hand and one for the SBC
• (2x) HDMI Breakout Board - one for the hand and one for the SBC
• (4x) Magnets
• (1x) Camera_Servo_Mount.stl
• (1x) SG90 Servo
• (1x) 8 MP Camera
• (8x) Pogopins - 6 pins for data, 2 pins for power
• (1x) Hand.stl

Hands Tools

The hand tools have 12v power and 6 data pins to the SBC. Current hand tools include a 1cc syringe pipetter, a magnetic whisker, a 405nm termination laser, and a UV-C Wand. Planned tools include ultrasonic homogenizer, microscope head for camera, gripper, and vacuum gripper.

• (1x) Hand-ToolAttachment.stl
• (4x) Screws
• (8x) Data Pads

User - Log into Cellerator

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Experiment Calendar - Manages concurrent running experiments and steps

Peer Review - A forum for discussion before, during, and after an experiment.

Under Development

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Sell Downtime - A market place to farm out parts of an experiment

Under Development

Data Analysis - A section to specify hypotheses, evaluate outcomes, compare hypotheses with real-time data views, and adjust protocols accordingly.

Under Development

ELN (Electronic Laboratory Notebook) - All steps, collected data, processed data, images/videos/time lapses, data processed images/videos/time lapse, stored into a simple to view HTML file.

Under Development

gCode Sender - Debugging Tool

Sequence Diagram 

Basic overview on how the user interacts with the computer and how the computer communicates with everything else.

Coding Syntax

The programming syntax is under development. 

The current implementation is that protocols are composed of steps, which are in turn composed of tasks.  The current programming syntax is called FAVR (Favor) .

FAVR

Function(Action, Inputs)[Verification][Record] 

Function is the main part of the code.  The user can pass either a hand, tool, calibrate, time tasks or logic.  Hand functions will be for water, air, vacuum.  Tool functions will be either hand tools or bench tools.  Calibrate function finds location of all tools, and sterilizes the build volume.  Time specified wait, do, and other basic intervals to sync with the Calendar.  Tasks are a combination of multiple FAVR commands.  And lastly logic, for, if, loop, etc. 

Action dictates the behavior of the specified Function.

Verification is usually set to 'Default' which will use the Action specified Verification, this can be camera images/stills/videos/time-lapse, QR Codes, or sensor data collected from hand tools and bench tools.

Record is usually set to ELN (Electronic Laboratory Notebook). This generates a real-time HTML with images, videos, collected data, and data points. Pages are served using a LAMP server.

Calibrate

Each protocol starts with calibration code. The calibrate code scans the build volume for QR Codes. The QR Codes are located on each tool and contain the QR code/tool location, volume measurement, and port location. Once scanned, the tool driver is updated with the current data. Future versions will include the UV-C Wand paint to sterilize the build volume before running an experiment.

X-axis contains

• (2x) X-axis_motor_mounts.stl
• (2x) Chrome linear motion rods
• (4x) Wheel assemblies

Y-Axis contains

• (2x) Y-axis_motor_mount.stl (LEFT) 
• (2x) Y-axis_idler_mount.stl (RIGHT)
• (2x) Stepper Motors
• Pulley Assembly

Z-axis contains

• (2x) Z-Axis_gantry_mount.stl
  
• (2x) Y-Axis linear ball bearing (YELLOW)

Z-axis Arm comprises

• (1x) Stepper Motor
• (1x) 8020 T-Slot Rail
• (1x) Z-Axis_motor_mount.stl
• (1x) 8mm Threaded Lead Screw
• (1x) Lead screw Coupler
• (1x) 8mm Thread Lead POM screw nut

Electronic Hardware

1. Raspberry Pi 4 (4 Gb)
2. Raspberry Pi Camera (8MP)
3. SG90 Servo (Tilt for Camera)
4. Arducam B0091 (CSI to HDMI breakout)
5. RJ11 (Bench tool communication via I2C protocol)
6. Shift Register (Control the 8 Channel Relay)
7. 8 Channel Relay ( Controls power for bench tools)
8. RGBW LEDs (Array of WS2912B LEDs)
9. Hand tool RJ45 (Hand tool communication via GPIO pins)
10. Arduino Uno R3
11. Arduino CNC Shield
12. Motor Controller (A4988)
13. Stepper Motors
14. End Stops

The proposed solution is a personal lab in a box. The box contains a robotic arm and eye. The arm is capable of interfacing with hand-tools and bench tools. A SBC (Single Board Computer) is used to control the robotic arm, record data from the digital camera, and interface with hand tools and bench tools. The combination of these elements will allow for cheaper experiments, easier skill sets based on software, and automation to free up time.

The box is 400x400x400mm in volume, with easy expansion in the X-direction. The box is a solid construction to keep water and clean air inside the box. The box is insulated to hold in incubation heat and dampen noise.

The robotic arm will be designed to utilize gCode, a widely adopted robotic instruction language. This language is used in additive manufacturing, CNC, and laser cutting. The drivetrain of the robotic arm is based on the Open Source Ecology 3D Printers. The hand tool system is modeled after FarmBots UTM (Universal Tool Mount).

The eye is an 8MP digital camera attached to a 180 tilt servo. The Servo and the Camera are connected to the SBC via an HDMI cord, capable of capturing still images, time-lapse, and video. These three formats can be used in parallel with image processing software.

Cellerator groups laboratory tools into two categories, hand tools and bench tools. Some common hand tools are pipetter, whisker, pH meter, magnetic wand and tweezers. Some common bench tools are scale, incubator, centrifuge, gel electrophoresis chamber, bioreactor, and affinity column. 

Cellerator has a hand to interface with hand tools. The hand contains a magnet coupler, RJ45, and power.  The magnets align to the hand tool and allow for docking.  The RJ45 port connects to 8 pogo pins, 2 pogo pins are for 12v power and ground, the other six pins are for communication to the GPIO pins. Future versions will incorporate water and airline. 

Bench tool contains ¼” diameter feet, RJ11 port, and power.  The bench contains an array of 1”x1”  ¼” holes and the bench tool is connected via pegs on the feet. The RJ11 port contains 4 pins, 2 pins are for 12v power and ground, the other 2 pins are for communication via I2C protocol.  Bench tools who need more than 12V have access to the power switch relay for power up to 120V.  Future versions will incorporate QR code that communicates QR code locations, device name, volume, and port locations.

Since we have observed that biotech is expensive, highly technical, and time-consuming, we want to lower the cost, simplify the needed skill, and automate labor-intensive tasks for anyone interested in biotech discoveries. This will lead to more discoveries in material, fuel, food, pharma, and medical science and the effect will be measured by the amount of generated publications.