Team:Carnegie Mellon/Hum-Circuit


Revision as of 00:43, 4 October 2012 by Ychoo (Talk | contribs)


Circuit Kit: Overview

In order to raise awareness, and motivate continued innovation in the field of synthetic biology, our iGEM team took the initiative to design a simple hardware demonstration platform, with which mentors can allow students to interact with a physical model of our project! The platform uses a microcontroller and a collection of simple circuits and components which communicate with a Matlab GUI to demonstrate how the various portions of our BioBricks interact to accomplish our goal.

Microcontrollers 101

Typically, microcontrollers are general purpose microprocessors which have additional parts that allow them to read, and control external devices. We often use the terms microcontroller and microprocessor interchangeably.

Microcontrollers are typically used to:
  • Gather sensor and component inputs.
  • Process these inputs, in digital format, to determine some output or action.
  • Utilize output devices and/or communication channels to do something useful.

  • Why use microcontrollers to help spread synthetic biology awareness? Microcontrollers are a good starting point for teaching students about general input/output systems, which are the primary design focus of synthetic biology: creating biological systems that transform environmental inputs into useful outputs. A basic microcontroller typically includes a microprocessor, digital inputs/outputs, analog inputs/outputs, and some type of communication interface (e.g., serial, wi-fi, bluetooth, etc.).

    Although our kit utilizes an off-the-shelf microcontroller (AtMega328P-PU based Arduino), we additionally designed a simplified version. This allows other collaborators and students to potentially replicate, or modify the project and eventually fabricate their own simplified microcontrollers for use in DIY synthetic biology education. In many senses, the BioBricks being developed through the iGEM foundation essentially function like minute microcontroller systems. It is thus important to identify this similarity, and provide students and future researchers with an opportunity to explore it.

    Simplified Microcontroller

    Below is a list of components used in our simplified microcontroller, and an image of the schematic designating the physical connections between the components and the AtMega328P-PU. These connections can initially be wired using a breadboard, which allows students to gain a simplified understanding of what connections are being made in off-the-shelf microcontrollers. If they choose, students can use the provided schematic files to order a PCB of their own from any of a variety of PCB manufacturers.

    Parts List:
  • AtMega328P-PU: ATMega328P-PU (AVR microcontroller)
  • IC2: 78L05 (5v Voltage Regulator, 100ma)
  • Q1: 16MHz Resonator (with internal capacitors)
  • C1: 0.1μF Capacitor
  • C2: 0.33μF Capacitor
  • C3: 0.1μF Capacitor
  • R1: 10KΩ Resistor

  • Simplified Microcontroller Schematic

    Simplified Microcontroller PCB Layout

    Follow this link to download the eagle schematic files. The link also contains a.) tutorial on how to wire up and program the simplified microcontroller on a breadboard from scratch (this should be accomplished prior to pcb manufacture) and b.) parts list for the project enclosure and supporting components.

    General Notes
  • Use the provided usb cable to connect the platform to a computer. Please do not detach the cable from the kit.

  • The GUI is implemented in Matlab currently, but will also be implemented via an open-source language.

  • Source-code for both implementations will be available via this link.

  • Overview
    The kit is comprised of one main BioBrick Unit (containing the programmed microcontroller) with interactive components, and an accompanying Fluorescence Unit which uses LEDs and a photo-resistor to emulate the process of collecting fluorescence microscope data. The LEDs illuminate with variable brightness in response to the user's choice of physical BioBrick configuration. This is roughly analogous to the fluorescence produced by cells illuminating in response to different BioBrick configurations in-vivo. The photo-resistor then emulates the fluorescence microscope by quantifying the light which is emitted by the LEDs. This "microscopy" process is paralleled by a Matlab GUI, which subsequently feeds the fluorescence data to the physical model, described here.

    Build a BioBrick

  • Insert the start-sequence, represented by the first set of 2-pin jumpers on the far left of the main unit.

  • Select a promoter from the 4 provided, and insert each promoter region.

    • A single promoter is composed of 3 promoter regions, represented by identically-colored resistors.
    • Note the orientation of the components when inserting each region.
    • The top resistor should connect slots 1 & 2. The middle resistor should connect slots 2 & 3. The bottom resistor should connect slots 3 & 4.
  • Insert the tRNA stabilizer headers (2).

  • Insert the Spinach sequence (6-pin header).

  • Insert both RBS & FAP sequences.

  • Insert the end-sequence, represented by the final set of 2-pin jumpers.

  • Characterize the Chosen Promoter

  • Open Matlab, and add the folder with the provided software to the Matlab path.

    • Right click the provided folder, and select "Add to Path -> Selected Folders and Sub-Folders"
  • Type "BioBrick_GUI" at the command prompt, and hit enter.

  • First, populate the time-step input table from top to bottom with the values 10, 20, 30, 40 ,50

  • Next, hit "Begin Time Lapse" at the top of the GUI:

    • Note that the software will first sweep through the entire range of all possible fluorescence input levels, and plot the measured fluorescence values.
    • Allow the program to run to completion, populating the output tables.
  • When the program is finished populating the outputs, hit "Calculate" to display the output values for translational efficiency and transcriptional strength.

  • To export the output tables to the Matlab workspace, select "File" from the menu bar, and choose "Export".

    • This will move the output tables, and calculated values to the workspace.
  • To plot an example comparison of the different promoters over time, enter "plot_data" at the Matlab command prompt.

    • Observe the plot_data.m function if you wish to plot your own data

    Make a Change and Observe the Effect!

  • Any of the following changes can be made to the BioBrick to help demonstrate the component relationships:
    • Remove the Spinach sequence,
    • Remove the tRNA stabilizer (one or both components),
    • Remove the RBS sequence, and replace with one of the 3-pin headers with blue wire (short),
    • Remove the FAP sequence, and replace with one of the 3-pin headers with blue wire (short),
    • Remove the START/END sequence,
    • Remove either DFHBI or MG by toggling the switches off (illuminated when 'ON'),
    • …or any combination of the previous.

    BioBrick Circuit Kit

    BioBrick Components

    BioBrick Main Unit Circuit Diagram

    BioBrick Fluorescence Unit Diagram