iGEM 2015 — Team Sherbrooke

# Team:Sherbrooke/Notebook

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# Notebook

| **Winter 2015** **Summer 2015** **Fall 2015** | | |
| --- | --- | --- |
| * [Week 1](#Week1) * [Week 2](#Week2) * [Week 3](#Week3) * [Week 4](#Week4) * [Week 5](#Week5) * [Weeks 6-8](#Week6-8) * [Week 9](#Week9) * [Week 10](#Week10) * [Week 11](#Week11) * [Week 12](#Week12) * [Week 13](#Week13) | * [Summer 2015](#Summer2015) | * [Week 14](#Week14) * [Week 15](#Week15) * [Week 16](#Week16) |

To ease project management, the BIOBOT team was separated in two distinct team called Instrumentation and Mechatronix. BIOBOT - Instrumentation was in charge of the TAC, MC1.5, MC96 and controller interface. BIOBOT - Mechatronix was in charge of the robotic platform, tool holder, pipettes handlers, centrifuge and BananaBoard. Here is a calendar of the work achieved, objectives fulfilled and problems encountered for both team, through each week from the beginning of the project. Although the whole team was subdivided as two entities, some of the work needed to be, and was, executed as a whole.

## Week 1

---

### Instrumentation

* **Done this week**
  + Initiation of the physical platform assembly
* **Objectives for the next week**
  + Start gathering information and knowledge
  + Continuing physical platform assembly
* **Problems encountered**
  + Team internal communications not efficient (Too many posts on the Facebook group page)

### Mechatronix

* **Done this week**
  + Definition of modules specifications
  + Choice of project management software. The web-application "LiteManagement", developed by one of the team's members.
* **Objectives for the next week**
  + Initiation of the physical platform assembly
  + Round up technical information for each modules
* **Problems encountered**
  + Dispatching the workload between team members

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## Week 2

---

### Instrumentation

* **Done this week**
  + Thinking about an efficient way to organise internal communications
  + First mechanical designs of the modules
  + First experimentations done on Peltier elements
* **Objectives for the next week**
  + First experimentations on magnets
  + Get the optic density circuit board up and running
* **Problems encountered**
  + No problems encountered

### Mechatronix

* **Done this week**
  + Identification of the different parts of the project
  + Prefeasibility study of the project
* **Objectives for the next week**
  + Build and test the robot platform
  + Preliminary design of the centrifuge
  + Preliminary design of the gripper
  + Preliminary design of the tool support
* **Problems encountered**
  + Low investment in hour from some team members
  + Misunderstanding of some parts of the required modules

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## Week 3

---

### Instrumentation

* **Done this week**
  + Preliminary mechanical design of the *MC96*
  + Finalizing the research on Peltier elements and photoreceptors
  + Choosing microprocessor used in each modules
* **Objectives for the next week**
  + Continuing experimentations on magnets
  + Finalize optic density circuit board
  + Starting to order parts for first prototypes
* **Problems encountered**
  + Disagreement with Mechatronix team about the microprocessor choice
  + Machining of some metal parts are too complex for the university's tools

### Mechatronix

* **Done this week**
  + Installation of the robot platform
  + Preliminary research for the centrifuge module
  + Preliminary research for the tool holder module
* **Objectives for the next week**
  + Preliminary conception of the centrifuge
  + Preliminary research for the tool holder
  + Preliminary research for the gripper
* **Problems encountered**
  + Poor management of the documentation
  + Documents quality issues
  + Disagreement with Instrumentation team about the microprocessor choice

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## Week 4

---

### Instrumentation

* **Done this week**
  + Experimentations and ordering of magnets
  + Modeling of the turbidity function
  + 3D modeling of all modules
  + Heat transmission simulation of the *TAC*
* **Objectives for the next week**
  + Heat transmission simulation of the *MC96* and *MC1.5*
  + Order Peltier elements
  + Peer review of team's performance
* **Problems encountered**
  + Difficult choice between multiples 3D designs for the *MC96*
  + Difficult choice between different types of magnets, due to many constraints (mechanical and physical)

### Mechatronix

* **Done this week**
  + Requirements analysis of the centrifuge
  + First preliminary design of the centrifuge
  + Research of the available technologies for the centrifuge
  + Research of the different motor types available
  + Research of the different types of sensor for the gripper
* **Objectives for the next week**
  + Preliminary conception of the gripper
  + Research and definition of the communication protocol between the modules
  + Installation of the motors for the X-Y movements of the platform
* **Problems encountered**
  + Delivery delays of some parts of the platform
  + Indecisive choice for the programming languages

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## Week 5

---

### Instrumentation

* **Done this week**
  + Heat transmission simulation of the *MC96* and *MC1.5*
  + Peltier elements received and characterized
  + Peer review of team's performance
* **Objectives for the next week**
  + Finishing Heat transmission simulation
  + Starting electrical plans for the *TAC*
* **Problems encountered**
  + Courses overlapping for four members of the team

### Mechatronix

* **Done this week**
  + Choice of the microprocessor: Psoc5
  + Preliminary design of the gripper
  + Assembly of the motors on the platform for the X-Y movements
  + Research on the available technologies for the centrifuge
* **Objectives for the next week**
  + Complete the information research on the tool holder
  + Complete the preliminary conception of the gripper and centrifuge modules
  + Continue the conception and design the gripper and centrifuge module
* **Problems encountered**
  + Some platform parts needed a 3D reprint
  + Most team members were overwhelmed by their courses

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## Week 6-8

---

### Instrumentation

* **Done these weeks**
  + Electrical design of the H-bridge for the Peltier element
  + First iteration of the User Interface
  + Peltier element heat transfer experimentation with an aluminium piece
  + Serial communication to the microprocessor
  + *TAC* function implemented on the microprocessor
* **Objectives for the next week**
  + Build the H-bridge circuit
  + Begin the electrical design of the module circuits
  + Adapt Psoc4 microprocessor code to Psoc5 microprocessor
  + Replace the air cooling system on the *MC96* with a more powerful liquid cooling system
  + Communication USB to User Interface
* **Problems encountered**
  + The heat sink does not dissipate enough heat from the Peltier element
  + First electrical design for the H-bridge not conclusive

### Mechatronix

* **Done these weeks**
  + Preliminary design of the gripper
  + Early detailed design of the gripper
  + First iteration of the Psoc code for the centrifuge
  + First iteration of the Psoc code for the gripper
* **Objectives for the next week**
  + Start the detailed conception of the electrical circuit of the modules
  + Finish the preliminary designs of the gripper and the centrifuge
  + Mechanical modeling of the gripper and the centrifuge
* **Problems encountered**
  + Tool holder design is more complex than anticipated
  + Too much weight on the tool holder causes undesired mechanical force on the robotic platform

[Back to top](#top_menu_under)

## Week 9

---

### Instrumentation

* **Done this week**
  + Simulation of Peltier Element electrical behaviour
  + Adapt Psoc4 microprocessor code to Psoc5 microprocessor
  + 3D Design of the liquid cooling system for *MC96*
  + Second iteration of the User Interface after review
  + Programming of the Raspberry Pi 2 in Python language
* **Objectives for the next week**
  + Building the H-bridge
  + Starting the PCB electrical design
  + Peltier element heat transfer experimentation with same aluminium piece as the *TAC*
  + Establish communication between User interface and microprocessor
* **Problems encountered**
  + Aluminium piece for the *TAC* arrived late
  + No electrical simulation model for desired H-bridge pieces

### Mechatronix

* **Done this week**
  + Conception of the Gripper controller with the Psoc microprocessor
  + Conception of the Centrifuge controller with the Psoc microprocessor
  + Determination and acquisition of the centrifuge motor
  + Detailed design of the centrifuge module
  + Interface of the Dynamixel motors with the Psoc microprocessor for the gripper
  + Interface of the coordinator (Rasberry Pi) with the SmoothieBoard
* **Objectives for the next week**
  + Continue the electrical circuit design (PCB)
  + Finish the interface of the coordinator with the SmoothieBoard
  + Start the CAN communication interface between the modules
  + Design the fixation of the gripper on the tool holder
* **Problems encountered**
  + The first choice of motor for the centrifuge was on back-order
  + Communication problems between the coordinator (RasberryPi) and the platform controller (SmoothieBoard)
  + Difficulties with the adaptation of the different interface/languages of the different parts of the project (main interface, database, etc.)

[Back to top](#top_menu_under)

## Week 10

---

### Instrumentation

* **Done this week**
  + Adapt PWM output of the H-bridge to a steady DC level for Peltier element
  + First TCP communication between User interface and Raspberry Pi 2
  + Peltier element heat transfer experimentation with same aluminium piece as the *TAC*
  + Starting programming of the Raspberry Pi 2 in Python language
* **Objectives for the next week**
  + Design a PCB to adapt the Banana Board output for Peltier element
  + Peltier element heat transfer experimentation with same aluminium piece as the *MC1.5*
  + Establish communication between User interface and microprocessor
* **Problems encountered**
  + New Peltier elements have not yet arrived

### Mechatronix

* **Done this week**
  + First iteration of the printed circuit board for the modules, the BananaBoard
  + Fine tuning of the platform controller for each axis motion
  + Tests on the centrifuge's motor
  + Implementation of a SPI to CAN converter for the coordinator
* **Objectives for the next week**
  + Continue the electrical circuit design (PCB)
  + Writing of a scientific article about our whole project
  + Validate the CAN communication protocol
  + Finish the mechanical design of the centrifuge
* **Problems encountered**
  + Unable to implement more than one Z axis on the robotic platform
  + Lack of documentation on the motor centrifuge
  + Driving the brush-less motor of the centrifuge is harder then expected

[Back to top](#top_menu_under)

## Week 11

---

### Instrumentation

* **Done this week**
  + Meeting with Acrolab Ltd. to discuss about heat pipe prototyping for the *MC96*
  + Improving User interface
  + Improvement of the 3D design of the *MC1.5*
  + Programming of the Raspberry Pi 2 in Python language
* **Objectives for the next week**
  + Design a temperature control algorithm for the *TAC*
  + Implementing the turbidity function in the *TAC*
  + Programming the microprocessor for the *TAC*
  + Finalizing the improvements of the 3D design of the *MC1.5*
* **Problems encountered**
  + Heat pipes very expensive (about 90$ per heat pipe)
  + Heat sinks have not yet arrived
  + Holes in the aluminium piece for the *MC1.5* are too tight for the 1.5 mL tubes

### Mechatronix

* **Done this week**
  + First manipulation with the robotic platform using the 3 axis of movement
  + Functional SPI communication within the SPI to CAN converter
  + Validation of the maximum RPM required with the centrifuge's motor
* **Objectives for the next week**
  + Finish the conception of the BananaBoard (PCB)
  + Programming and tests of the Psoc controller for the gripper
  + Programming and tests of the Psoc controller for the centrifuge
  + Order missing parts of the centrifuge and tool holder
  + Write the address tables for the CAN bus
  + Finish the redaction of the scientific article
* **Problems encountered**
  + Delay in the conception of the BananaBoard (PCB)
  + More functions and parts than planned for the BananaBoard which had to be added

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## Week 12

---

### Instrumentation

* **Done this week**
  + Prototype circuit for the turbidity function of the *TAC*
  + Implementation of the turbidity algorithm in C language
  + Shopping for a new linear actuator
  + Modeling of the thermal system of the *TAC*
  + Improving User interface
* **Objectives for the next week**
  + Design a temperature control algorithm for the *TAC*
  + Implementing the turbidity function in the *TAC*
  + Programming the microprocessor for the *TAC*
* **Problems encountered**
  + One Peltier element was faulty
  + The remaining Peltier element emit too much heat for the available heat sinks
  + Problems with the Psoc5 libraries

### Mechatronix

* **Done this week**
  + The BananaBoard (PCB) design is complete
  + User interface in C# for the gripper
  + Controller for the gripper with the Psoc is complete
* **Objectives for the next week**
  + Validate the BananaBoard design
  + Order the BananaBoards
  + Write the address tables of the CAN bus
  + Detailed design of the tool holder
* **Problems encountered**
  + Ordered parts were back-order which caused delivery delays
  + Delays in the design of the tool holder
  + Different actions of the tool holder more complex than anticipated

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## Week 13

---

### Instrumentation

* **Done this week**
  + Calibrating the turbidity measurements in the *TAC*
  + Shopping for a new linear actuator
  + Correcting the 3D design of the *TAC*
  + Correcting the 3D design of the *MC1.5*
  + Improving User interface
* **Objectives for the next week**
  + Design a temperature control algorithm for the *TAC*
  + Integrating multiple functions of the *TAC* on the microprocessor
* **Problems encountered**
  + Work time shortened by semester's finals

### Mechatronix

* **Done this week**
  + Validation and corrections of the BananaBoard design
  + Test and proof of functionality of the gripper
  + Machining of the centrifuge mechanical parts
  + Revision of the design of the tool holder
* **Objectives for the next week**
  + Design review of the BananaBoard
  + Finalizing the Psoc controller for the centrifuge
  + Order and assemble the parts for the new design of the tool holder
  + Write the address tables of the CAN bus
* **Problems encountered**
  + Work time shortened by semester's finals
  + The weight of the platform is considerable and unevenly distributed

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## Summer 2015

---

### Instrumentation

* **Done during Summer**
  + Implementation of the database for the protocols and the modules functionalities
  + Help Mechatronix to built the second iteration of the platform
  + Communication between the database and the User interface
  + Minor reworking of 3D models for all modules
  + *MC1.5* test tube aluminium mold received
  + Implementation of individual function on the *TAC*
* **Objectives for the end of the summer**
  + Platform functional
  + Implementing CAN communication
* **Problems encountered**
  + Half of the team's members were out of town for the summer working(internships)

### Mechatronix

* **Done during Summer**
  + Programming of CAN communication protocol
  + BananaBoard PCB debugging and beginning of soldering
  + Building of the second iteration of the platform
  + 3D drawing for the centrifuge
  + Building of the tool-holder
  + Writing of the Wiki Web-Site for the iGEM competition
  + Sponsorship research
* **Objectives for the end of the summer**
  + Interface the gripper on the platform
  + Solder the last BananaBoard PCBs
  + Machining the centrifuge's pieces
  + Machining and assembling the pipette modules
  + Sponsorship research
* **Problems encountered**
  + Half of the team's members were out of town for the summer working(internships)

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## Week 14

---

### Instrumentation

* **Done this week**
  + Platform assembled
  + Testing power supply for the modules
  + 3D printing of the *MC1.5*
  + Recording on the EEPROM of the microprocessor
  + Temperature control calibration implemented
  + Data base in the program implemented
* **Objectives for the next week**
  + Implement CAN communication
  + Program BananaBoard
  + Populate database
* **Problems encountered**
  + Pieces missing for the platform

### Mechatronix

* **Done this week**
  + Platform assembling was completed
  + Tool-Holder assembling was completed
* **Objectives for the next week**
  + Complete debugging and soldering of the BananaBoards
  + Complete pipettes pieces machining and start pipettes assembling
  + Complete centrifuge pieces machining
  + Interface the gripper with the platform
  + Continue our team Wiki page for iGEM competition
  + Sponsorship research
* **Problems encountered**
  + One team member hadn't returned to Sherbrooke yet
  + Pieces missing for the platform
  + Not yet able to program BananaBoard's microprocessor
  + Pipettes' mechanical design and machining took longer than expected

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## Week 15

---

### Instrumentation

* **Done this week**
  + Communication established between the PC and the platform
  + CAN communication implemented on the BananaBoard
  + Adaptation of a 3D printer controller for the control of the platform
  + Attempt to "home" the Z axis
  + Adjusting the screw shaft for the X and Y axis
  + Link between the database and the user interface
* **Objectives for the next week**
  + Execute an entire protocol on individual module
* **Problems encountered**
  + No connector for programming the BananaBoard microprocessor
  + No homing function implemented in the 3D printer controller

### Mechatronix

* **Done this week**
  + Debugging, soldering and programming of BananaBoards for the centrifuge, *TAC* and *MC1.5*
  + Soldering of BananaBoard for the gripper and pipettes
  + Programming of centrifuge software on a development board
  + Machining of centrifuge pieces
  + Mechanical support of the gripper for the tool-holder designed
  + Continue our team Wiki page for iGEM competition
* **Objectives for the next week**
  + Install pipettes on the tool-holder
  + Debugging and programming of the BananaBoards for the gripper, centrifuge and pipettes
  + Testing of pipette
  + Test centrifuge functions
* **Problems encountered**
  + Pipettes' mechanical design and machining took longer than expected
  + Centrifuge's pieces machining takes longer then expected

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## Week 16

---

### Instrumentation

* **Done this week**
  + Faster movement for the platform
  + Turbidity interface for *TAC* module
  + 3D design of the platform on SolidWorks
  + Standardisation of the CAN communication
  + Creation of a protocol in the user interface
* **Objectives for the next week**
  + Run a protocol on the platform
* **Problems encountered**
  + Implementation of a firmware for the microprocessor

### Mechatronix

* **Done this week**
  + Single and multi-channel pipette mechanical assembly
  + Soldering and Debugging of last PCBs
  + Pipettes' PCB programming
  + CAN and motor control of the centrifuge
* **Objectives for the next week**
  + Pipettes operating tests
  + Debugging and programming of gripper's BananaBoard
  + Pipetting tests and calibration
  + Modules CAN communication
* **Problems encountered**
  + Electrical signal problems with the gripper's BananaBoard

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