Team:Sherbrooke/Design
Hardware Design
Our robotic platform consists of many modules, each with their own design, specifications and functionalities. Each module is independent and can either be operated alone or in combination with other modules. The teamwork between every module is managed by the Main Administrator, which communicates and controls them via a CAN communication bus and custom controller boards created by our team, that we named "BananaBoard. Currently, the project comprises nine distinct modules: the platform, the tool holder, custom pipettes (one single and one multi-channel), the gripper, the centrifuge, and the turbido agitator caloric module for glass tube (TAC), the magneto caloric module for 1.5mL tube (MC1.5), and the magneto caloric module for 96-well plate (MC96). Most of our modules are controlled by our "BananaBoard". There is also a controller interface for the user so he can create and automate his protocols. The global architecture of the robotic platform is as follows:
BIOBOT: Global Project Architecture
In this page you will learn all there is to know about each module, whether it is for the electrical, mechanical or software design. Scroll down or choose one module in the following list to learn about it.
Modules
- Platform
- Tool Holder
- Pipettes
- Gripper
- Centrifuge
- Magneto Caloric 1.5 (MC1.5)
- Turbido Agitator Caloric (TAC)
- Magneto Caloric 96 (MC96)
- BananaBoard
- Controller Interface
Platform
Description
The physical platform consists of everything related to the structure on which the movements take place. It also acts as the reference surface area for the labware and modules used during a protocol. It is equipped with motors and traction mechanisms for movement on the horizontal plane, as well as indicators to locate the home position of each axis. The top of the structure is a travelling bridge for a trolley with the tool holder attached to it. The movements and limit detection of the platform are supervised by an Arduino controller board with a Marlin Ramps 1.4 shield coded a custom firmware in it. The platform motors are driven in current by 2 MKS TB6600 V1.1. The robot does smooth and precise movements and gives feedback on its position on demand.
Robotic Platform
The frame is made up of aluminum extrusions. This material was selected due to its lightweightness, rather low cost, easy of manipulation, and simplicity to sterilize. When designing the platform, we sometimes created a first version of some parts using a 3D printer to validate our concept. After validation, most of those parts were replaced by a machined aluminum version.
Movements of the different axes are driven by stepper motors to perform translations of the travelling bridge and of the trolley. For movements relative to the horizontal plane, two NEMA 23 stepper motors, model 17HS3001-20B, were used. They offer fast speeds, while still being precise to 0.008 mm, which is useful to move the tools to a precise position without slowing down the whole process. They were also chosen because of their durability and reliability. Those two assets are significant since a lot of repetitive movements occur in the horizontal plane, which consequently deals with more wear and tear. These motors are coupled with an endless screw which makes the assembly move as the motors spin.
Specifications
Mechanical
| Specification | Value |
|---|---|
| Frame material | Aluminum extrusions |
| Dimensions | 160 cm x 120 cm x 130 cm |
| Motion mean | Stepper motors coupled with endless screws |
| X axis movement precision | 0.127 mm |
| X axis movement speed | 0 to 500 mm/s |
| Y axis movement precision | 0.127 mm |
| Y axis movement speed | 0 to 500 mm/s |
Electrical
| Specification | Value |
|---|---|
| Motors' input voltage | 24V |
Software
| Specification | Value |
|---|---|
| Language | C++ |
Parts list
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Assembly
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Tool Holder
Tool Holder Front View
Tool Holder Back View
Description
One of the main objective of the platform is to perform pipetting operations using different type of pipettes, namely, single-channel and multi-channel pipette. To hold and use them, a custom tool holder was designed and built. The holder is fixed on the trolley which is fixed on the travelling bridge. The tool holder has three independent C-Beam by OpenBuilds to perform movement along the vertical axis. The two first C-Beams are used for pipette and the third one is used for the gripper. Pipettes' C-Beams are equipped with a syringe holder, made of stepper motors to press or pull the syringe's piston and aslo to hold the BananaBoard. All the C-Beams' motors are controlled and driven in current like the platform's motor: with an Arduino controller board with a Marlin Ramps 1.4 shield which is programmed with our custom firmware in it.
Specifications
Mechanical
| Specification | Value |
|---|---|
| Frame material | Aluminum extrusions |
| Dimensions | X cm x X cm x X cm |
| Motion mean | Stepper motors coupled with endless screws |
| Z axis movement precision | 0.4 mm |
| Z axis movement speed | 156 mm/s |
Electrical
| Specification | Value |
|---|---|
| Motors' input voltage | 24V |
Software
| Specification | Value |
|---|---|
| Language | C++ |
Parts list
- 3x C-Beam Linear Rail, 500mm
- 3x NEMA 23 Stepper Motor, Model: Motech Motor, MT-2303Hs280AW-0B, 1.8°/Step
- 3x C shaped rails, 500mm
- 3x Endless screw, 500mm
- 2x XX Motor pour le pipettage
Assembly
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Pipettes
Single-Channel Pipette
Multi-Channel Pipette
Description
Pipetting is one of our platform major functionality. To do so, we designed custom pipette modules using syringes equipped with a versatile tip adapter capable of loading tips of different size (2&mul, 200&mul and 1000&mul) on the same adapter. This will give our pipette system more versatility. Using custom pipette modules has ease the design of the mechanical interface between our pipettes and the tool-holder. We designed a single-channel pipette as well as a multi-channel one (8 channels).
The system is somewhat simple. A custom support was designed and machined in aluminum pieces to hold the different parts of the whole pipette system. Starting at the bottom, a pipette tip is fixed on adapter. This adapter is needed because pipette tips are not design to fit on syringe and vice versa. Attached on top of the adapter is the syringe. The syringe piston is grabbed by a mechanical piece that is coupled on an endless screw, which is coupled on a stepper motor. As the motor spins, the piston moves in the syringe, and doing so, vacuuming the liquid in and out of the pipette tip. The amount of liquid in the pipette is known and controlled by the number of step the motor spins. The whole pipette assembly is then fixed on the tool-holder and is controlled by a BananaBoard.
The multi-channel pipette system has a minor difference, beside the number of syringe and tip of course. Because it was not possible to assemble the syringes close enough so they would fit the width of a standard 96-well plate, we had to add tubing between the syringe and the pipette tip adaptor. That way, the tip adaptor is close enough to fit a standard 96 tips box, and there is enough space to attach the larger syringes side-by-side. Take a look at the assembly section of the pipette to have a better idea of the system.
Specifications
Mechanical
| Specification | Value |
|---|---|
| Dimensions (Height Width x Depth) | Single channel: 283 mm X 80 mm X 52 mm Multi channel: 224.2 mm X 175 mm X 99 mm |
| Vacuuming range | 0 to 1000 μl |
| Vacuuming precision | 0.2 μl |
Electrical
| Specification | Value |
|---|---|
| Stepper motor's input voltage | 12V |
Software
| Specification | Value |
|---|---|
| Language | C++ |
Parts list
- Idex P-420 Super Flangeless Female Nut PEKK Natural for 1/16" OD (link)
- Idex P-259 Super Flangeless Ferrule w/SST Ring, Tefzel (ETFE), 1/4-28 Flat-Bottom, for 1/16" OD (link)
- Idex XP-286 Flangeless Fitting Headless, PEEK, Natural, 1/4-28 Flat-Bottom, for 1/16" OD (link)
Assembly and Bill of Material
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Gripper
Gripper
Description
The finger-like gripper is design to allow the handling of lab-ware around the work area. It can moves tubes, micro-plate and different type of containers or boxes such as pipette tip box around as needed. The gripper is fixed to one of the three z-axis of the tool holder. It can therefore be used independently of the other tools on the holder. The gripper first consists of a Dual Gripper Kit obtained from Crust Crawler Robotics. This kit uses two Robotis' Dynamixel AX-12A servomotors for the finger-like motion. We then added a third AX-12A servo to give the gripper wrist-like capabilities, adding flexion and extension movement. Lastly, a MX-12W servo was also added so the gripper can rotate around a vertical axis on 360°.
This gripper kit was chosen because it uses Robotis' Dynamixel servomotors. Those servos are easy to control and their precision in movement allows the gripper to access almost any components. They offer various options to monitor and use different operating values of the servo even during live operation, allowing us to use them at our will to control the gripping function of our platform. The most useful Dynamxiel's control function is the torque limit that we can set to a custom value corresponding to the object we desire to grip. Also, the MX-12W was chosen for the gripper rotation because the angle of the servo can be monitored over 360°, unlike AX-12A Dynamixel which can only be monitored from -150° to 150°. The servos assembly gives the gripper the ability to take narrow objects as well as wider ones, and it can grip them from top or from the side. It can also rotate on 360°. The gripper is controlled by a dedicated BananaBoard.
Specifications
Mechanical
| Specification | Value |
|---|---|
| Dimensions | 258 mm x 75 mm x 97 cm |
| Motors | Robotis' Dynamixel AX and MX servomotors |
| Fingertip precision | 0.7 mm |
| Fingertip speed | from 0 to 680 mm/s |
| Fingertip torque | from 0 to 1.5 N*m |
| Rotation precision | 0.088° |
| Rotation speed | from 0 to 470 rpm |
Electrical
| Specification | Value |
|---|---|
| Servos' input voltage | 12V |
Software
| Specification | Value |
|---|---|
| Language | C++ |
Parts list
- 3x Dynamixel AX-12A by Robotis (link)
- 1x Dynamixel MX-12W by Robotis (link)
- 1x CrustCrawler AX Dual Robotic Gripper Hardware Kit (link)
- 2x Bioloid F2 Frame (from Dynamixel servo's kit)
- 3x Bioloid F3 Frame (from Dynamixel servo's kit)
- 3x 3-Pins Dynamixel Communication Cable (from Dynamixel servo's kit)
- Bolts and nuts (from Dynamixel servo's kit)
Assembly
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Centrifuge
Centrifuge
Description
Centrifugation operations are often required for protocols in molecular biology labs and that is why we wanted to build a custom automated centrifuge that can be operated with the platform and the gripper.
The centrifuge is able to fit up to eight 1.5 ml tubes and up to four 5 ml tubes. The rotating plate, which hold the tubes, is made of polyoxymethylene, a lightweight and strong thermoplastic. It is coupled on a Quanum MT series 2208 brush-less DC motor. Such motors offer high rotation speed and compact size, two characteristics important for the whole design. Swinging bucket tube holders allow tube to be in a vertical position when resting, to ease manipulation with the gripper, and force tube to tilt to a 45° angle during centrifugation so the pellet forms at the bottom of the tube and not on the side. To detect high vibrations, a warning of potential problems during run-time, an accelerometer is added to the module and stops the centrifuge if needed to prevent any accident. The centrifuge is equipped with an automated lid which is secured by a lock mechanism during running time. Because the lid only opens over one tube slot, we need to rotate the plate from slot to slot when the centrifuge is being loaded by the gripper. To do so, a magnetic sensor is positioned on the axis of rotation so the absolute angular position is known. That way, it is possible to rotate the plate to place a tube slot under the opening in the lid so the gripper can load and unload tubes. The magnetic sensor is also use to measure the rotation speed of the centrifuge. And of course, the whole centrifuge case is built with a sturdy construction, using material such as aluminum and polycarbonate to prevent any external damage should there be any internal problems. The centrifuge is controlled by a dedicated BananaBoard.
Specifications
Mechanical
| Specification | Value |
|---|---|
| Dimensions (Length x Width x Height) | 209 mm x 209 mm x 182 mm |
| Rotation Speed | 16 500 rpm |
| G Force applied | 18000 G |
| Tube capacity | 8x 1.5mL tubes and 4x 5mL tubes |
Electrical
| Specification | Value |
|---|---|
| Motor's input voltage | 12V |
Software
| Specification | Value |
|---|---|
| Language | C++ |
Parts list
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Assembly
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Magneto Caloric 1.5 (MC1.5)
Description
MC1.5 3D Plan
The other module that can control temperature and magnetic field is called Magneto Caloric 1.5 (MC1.5) and has the same functionalities as the MC96, but for tubes containing an amount of liquid as high as 1.5mL, which is more than the capacity of a MC96 well. The MC1.5 consists of two independent sub-modules. So, each sub-module could have its own sequence.
Specifications
Thermal
| Specification | Value |
|---|---|
| Range | Achieved 4 to 80°C |
| Precision | Achieved ±1.5°C |
| Heating speed | Achieved 1.81°C/s |
| Cooling speed | Achieved 0.5°C/s |
Mechanical
| Specification | Value |
|---|---|
| Material | 1.5ml test tube mold : Aluminium Frames and Module base : Plastic |
| Dimensions | 8.5cm x 12.8cm x 22 cm |
| Linear actuator speed | 12mm/s |
| Linear actuator stroke | 2cm |
Electrical
| Specification | Value |
|---|---|
| Input voltage | 24V |
| Maximal power consumption | ≈400 Watts |
Software
| Specification | Value |
|---|---|
| Language | C++ |
Parts list
Download Bill of Material File
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Turbido Agitator Caloric (TAC)
Description
TAC 3D Plan
The main function of this module is to grow cell culture in a 25mm test tube. To do so, the module must regulate the tube temperature, be able to agitate the liquid and to measure the amount of cells in the culture. The TAC module enables the automation of repetitive steps that are performed on a daily basis in laboratories around the world. It can be reprogrammed to meet specifications of different protocols for molecular biology or microbiology experiments.
One possible application of the TAC module would be the insertion of DNA into a micro-organism. This manipulation requires the growth of the micro-organism at the optimal temperature until a specific optical density is reached. This is required for the observed colony to enter its stationary phase as we can observe in the following figure.
Cell density of a culture vs time
Once the optical density has been reached, the cells have to be washed a couple times to eliminate the residual growing media. Afterwards, the DNA is added to the mix and the cells are perforated to allow its transfer. This stressful operation kills most of them. Therefore, we have to replicate them quickly in a proper medium and at the right temperature.
To regulate the temperature between 0 and 37°C, a Peltier element is used because it can heat or cool the tube depending on the current’s direction. An heat sink is stick to the other side of the Peltier element to eliminate the heat produced by the Peltier element. The fan is used to create a forced convection, thus increasing the efficiency of the heat sink.
To agitate the liquid, the same principle as a magnetic stirrer is used. First, a magnetic stirrer bar must be inserted into the test tube. Then, a magnet stuck on a DC motor attracted the magnetic stirrer bar. So, when the DC motor rotates the magnetic stirrer bar inside the test tube rotates at the same speed and thus, agitating the liquid.
To measure the amount of cells in the culture, a system has previously been developed by the lab of professor Rodrigue. This system used the transmittance of the liquid to measure the amount of cells in a 25mm test tube. To measure it, a LED (light-emitting diode) is placed on one side of the test tube and a photodiode is placed on the other side. The LED blinks and this blink is received on the photodiode, generating a square signal as shown in the folowing Figure.
Photodiode signal voltage vs time
The amplitude difference between the signal high and the signal low increase as the transmittance increased and decreased as the transmittance decreased. A calibration graph has been calculated and is shown in the folowing Figure.
Optical density vs Amplitude difference
Specifications
Thermal
| Specification | Value |
|---|---|
| Range | 0 to 37°C |
| Precision | ±1.5°C |
| Heating speed | Achieved 1.2°C/s |
| Cooling speed | Achieved 0.3°C/s if tube temperature above room temperature Achieved 0.21°C/s if tube temperature below room temperature |
Mechanical
| Specification | Value |
|---|---|
| Material | 25mm test tube mold : Aluminium Frames and Module base : Plastic |
| Dimensions | 8.5cm x 12.8cm x 21.8cm |
| DC motor speed | 60 to 600 rpm |
Electrical
| Specification | Value |
|---|---|
| Input voltage | 24V |
| Maximal power consumption | ≈400 Watts |
| Turbidity measurement precision | ±5% from a reference turbidimeter |
Software
| Specification | Value |
|---|---|
| Language | C++ |
Parts list
Download Bill of Material File
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Magneto Caloric 96 (MC96)
Description
MC96 3D Plan
This module is called Magneto Caloric 96 (MC96) because it has to manage magnetism and temperature cycling (caloric) of a 96-well plate. The main use of the MC96 is to apply a specific temperature on different liquids (e.g. cell cultures) in the context of biological research.
The module has the possibility to concentrate particles in a solutions by applying an electromagnetic field that will bring particles on the wall of the well. This is explained by the magnetic attraction of microscopic magnetic beads to which particles are agglomerated. The beads are to be introduced into the well during the procedure and this can also be automated.
To apply the electromagnetic field, neodymium magnets are moved to the side of the wells. To do so, the magnets are assembled in a frame that is moved by a linear actuator. So, when the actuator raises the frame, the magnets are moved near the wells and the beads are brought on the well’s wall.
To implement thermal cycling, a Peltier element is used because it can heat or cool the 96-well plate depending on the current’s direction. A heat sink is stick to the other side of the Peltier element to eliminate the heat produced by it. The fan is used to create a forced convection, thus increasing the efficiency of the heat sink.Specifications
These characteristics are the desired specifications or part’s characteristics because no prototype has been built yet.
Thermal
| Specification | Value |
|---|---|
| Range | 4 to 80°C |
| Precision | ±1.5°C |
| Heating speed | 0.5-1°C/s |
| Cooling speed | 0.5-1°C/s |
Mechanical
| Specification | Value |
|---|---|
| Material | 96-well mold : Aluminium Frames and Module base : Plastic |
| Dimensions | 12.8cm x 13.34cm x 18.43cm |
| Linear actuator speed | 12mm/s |
| Linear actuator stroke | 2cm |
Electrical
| Specification | Value |
|---|---|
| Input voltage | 24V |
| Maximal power consumption | ≈800 Watts |
Software
| Specification | Value |
|---|---|
| Language | C++ |
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BananaBoard
BananaBoard Top and Bottom view
Description
With so many different independent modules, it would have been a real struggle to design a Printed Circuit Board (PCB) for each of them. Yet, when you compare modules to each other, you can notice that there are similarities between them. We therefore decided to design a single PCB (that we named BananaBoard) that has all the electrical and software capabilities to supply every modules individually. The components soldered on te BananaBoard depend on the module interfaced with the PCB. For example, the BananaBoard has a 24V output connectors. The gripper doesn't need this electrical supply but the MC1.5 and the TAC need it. So the component for this output will not be soldered on the PCB for the gripper, but they will be for the MC1.5 and the TAC's PCB. This allowed us to save design time and reduce complexity during the PCB assembly and debugging. The BananaBoard is also versatile enough so it could be used if new modules are design or if existing equipment from third party must be integrated on the platform.
Specifications
Mechanical
| Specification | Value |
|---|---|
| Dimensions (with all component soldered) | 107.9 mm x 80.4 mm x 35.8 mm |
Electrical
| Specification | Value |
|---|---|
| Input voltage | 12-24 V |
| Output voltages | 12-24 V / 60 A: Half H-Bridges and Stepper Motors 5 V / 1 A: Logic Circuit, LED, Sensors 3.3 V / 100 mA: Accelerometer |
| Microcontroler | Cypress' PSoC5 CYC5868AXI-LP034 |
| Other components |
|
Software
| Specification | Value |
|---|---|
| Language | C++ |
Parts list
...
Assembly
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Controller Interface
Description
The controller interface is used to control the platform as well as the modules installed on it. The controller interface is hosted on a PC connected to the platform via a USB to CAN converter. The following figure shows the interface:
Controller Interface
| # | Close-up | Desciption |
|---|---|---|
| 1 |  |
This is the menus of the interface. The File menu allows the user to import and save protocols, module definition, deck layout and more. The Options menu allows the user to is to modify and configure USB communication, platform and modules variable and more. |
| 2 |  |
This is a list of selected protocols. This allows the user to start and stop the selected protocol. To add a protocol simply drag the protocol from Steps to Protocols. |
| 3 |  |
This is a list of protocols that have been created or have been imported. A protocol is a collection of commands (steps) that can be sent to the platform. A protocol could also contain another protocol. For example, there is protocol named “Grow” and another protocol named “Pipetting”. The user can then create a new protocol named “Grow and Pipetting” containing “Grow” and ”Pipetting”. It is possible to add a protocol by clicking on Add. |
| 4 |  |
This is a list of available tools on the platform. This allows the user to edit the parameters of the modules present on the platform by clicking on Edit. The user can also access this feature in the Options menus. |
| 5 |  |
This is the deck layout. This allows the user to represent the actual position of different modules on the platform. To add a module on the deck, it has been planned to drag it from the tools list. |
| 6 |  |
This is the connection indicator. This allows the user to know whether or not the host PC is connected to the platform. |
| 7 |  |
The is the labware list. This list allows the user to register all labware item, like 96-wells plate, 25mm test tube or pipette tips. |
| 8 |  |
This is the console. The console allows the user to see every important events occurring on the platform. This also allows the user to directly send a message to the platform by typing it into the field under the log then click on the Send button. It is planned to implement this feature after the competition. |
Specifications
Software
| Specification | Value |
|---|---|
| Language | C# |
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