Team:Carnegie Mellon/Hum-Circuit

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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Team">Team</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Attributions">Attributions</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Matlab">Matlab</a>
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Matlab">Matlab</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Expanded">Expanded</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Overview">Human Practices</a>
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Overview">Human Practices</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Overview">Overview</a>
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Overview">Overview</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Software">Software</a>
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Software">Software</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Team">Team Presentation</a>
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Teaching">Teaching Presentation</a>
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<li><a href="#section1-2">1.2 Question 2</a></li>
<li><a href="#section1-2">1.2 Question 2</a></li>
<li><a href="#section1-3">1.2 Question 3</a></li>
<li><a href="#section1-3">1.2 Question 3</a></li>
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<li><a href="#section1-4">1.2 Question 3</a></li>
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<h1 id="section1-1">Circuit Kit: Overview </h1>
<h1 id="section1-1">Circuit Kit: Overview </h1>
<p>
<p>
-
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 to demonstrate how the various portions of our BioBricks interact to accomplish our goal.  
+
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. <br>
 +
Most importantly, we hope all iGEM teams can take inspiration from our experiences and build similar electric analogs of their BioBricks designs! We've found them to be an amazing tool for engaging high school students and piquing their interest and understanding in Synthetic Biology.
</p>
</p>
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<h1 id="section1-2">Microcontrollers 101 </h1>
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<h1 id="section1-2">Microcontrollers 101: </h1>
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<p>
<p>
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.  
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.  
</p>
</p>
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<img src="https://static.igem.org/mediawiki/2012/6/6f/CMU_Arduino.jpg" height="287" width="287" align="right" alt="Matlab BioBrick GUI"/>
<b> Microcontrollers are typically used to: </b>  
<b> Microcontrollers are typically used to: </b>  
<li> Gather sensor and component <i>inputs</i>. </li>
<li> Gather sensor and component <i>inputs</i>. </li>
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<li> Utilize output devices and/or communication channels to do something useful. </li>
<li> Utilize output devices and/or communication channels to do something useful. </li>
<br>
<br>
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<p>
<p>
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Why use <i>microcontrollers</i> 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).  
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Why use <i>microcontrollers</i> 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: <b>creating biological systems that transform environmental inputs into useful outputs</b>. 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.).  
</p>
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<h1 id="section1-3">Simplified Microcontroller: </h1>
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<h1 id="section1-3">Simplified Microcontroller </h1>
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<p>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.  
+
<p>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.  
</p>
</p>
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<br>
<br>
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<b>Simplified Microcontroller Schematic:</b><br>
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<b>Simplified Microcontroller Schematic</b><br>
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<img src="https://static.igem.org/mediawiki/2012/a/a7/Schematic_PCB_MCU.png" height="300" width="433"/>
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<img src="https://static.igem.org/mediawiki/2012/a/a7/Schematic_PCB_MCU.png" height="450" width="650"/>
<br><br>
<br><br>
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<b>Simplified Microcontroller PCB Layout</b><br>
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<img src="https://static.igem.org/mediawiki/2012/c/c5/Schematic_PCB_Layout.png" />
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<br><br>
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<p>
 +
Follow this <a href="https://www.dropbox.com/sh/nb9cs0gpbvlrpxa/PMXNzM1p7G"> link</a> 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.
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<br><br>
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</p>
</section>
</section>
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        </div>
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    </div>
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<h1 id="section1-2"> System implemented with the kit </h1>
 
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<img src="https://static.igem.org/mediawiki/2012/f/f4/System_model.jpg" height="300" width="433" align="right"/>
 
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                <p>
 
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                As described <a href="https://2012.igem.org/Team:Carnegie_Mellon"> here</a>, our team engineered a fluorescence-based sensor that provides information on both transcription strength and translation efficiency of a promoter. The sensor is noninvasive, easily applied to a variety of promoters, and capable of providing results in a time frame that is short when compared to current technologies for the characterization of promoters. 
 
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                </p>
 
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                <p>
 
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The sensor is based on the use of an RNA aptamer (termed Spinach) and a fluorogen activating protein (FAP). The complexes of Spinach (mRNA-DMHBI in the Figure) and FAP (FAP-MG in the Figure) with specific dyes, DFHBI and MG, respectively, are fluorescent. Measurements of the fluorescence intensity of these complexes enables one to determine the concentration of mRNA and expressed protein for a given promoter. Analysis of the fluorescence data with an appropriate model leads to the transcription strength and translation efficiency for each promoter.
 
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            </section>
 
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     <div id="wrapper">
     <div id="wrapper">
     <header id = "header">
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<h1 id = "section1-3">
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  The hardware/software platform
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<h1 id = "section1-4"> Using the Hardware/Software Platform </h1>
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</h1>
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             <header id = "header2">
             <header id = "header2">
<img src="https://static.igem.org/mediawiki/2012/a/a9/Circuit_kit.jpg" height="300" width="500" align="right"/>
<img src="https://static.igem.org/mediawiki/2012/a/a9/Circuit_kit.jpg" height="300" width="500" align="right"/>
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The goal was to create a model of our <b><a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Derivations"> biosensor</a></b> that clearly represents its main components and makes clear how the biosensor works.  We also planned to enable the students to simulate changes in the “environment” and to observe the outcome of these changes.  To achieve this goal, we built an affordable, microcontroller-based, <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Documentation"> hardware</a> platform and also developed an associated, open-source, simulation <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Software"> software</a>.
 
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</p>
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 +
<b> General Notes </b>
 +
<ol>
 +
<li> Use the provided usb cable to connect the platform to a computer. Please do not detach the cable from the kit. </li>
 +
<li> The GUI is implemented in Matlab currently, but will also be implemented via an open-source language.</li>
 +
<li> Source-code for both implementations will be available via this <a href="https://www.dropbox.com/sh/zeeugv3pt4pgo0l/JkQ47msyeM"> link</a>. </li>
 +
</ol>
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<br><br>
 +
 
 +
 
 +
<b> Overview </b><br>
 +
 
<p>
<p>
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The combined hardware/software platform allows the students to directly manipulate electronic components, which are formal equivalents of the BioBricks used in our sensor, and to observe the effect of changing these components on the current or voltage output, which is the equivalent of the fluorescence intensity in our lab experiments. In using the kit, the students get a feel for how different promoters are compared using the biosensor; they can rank "virtual promoters" in the order of their strength. Students who use the kit gain hands-on experience and understand how all the parts of the biosensor work together to measure the mRNA and protein levels, without working in the wet lab.
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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 <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Overview"> here</a>.
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The figure on the right is a photograph of the hardware platform on which the correspondence between the biological components of the biosensor and the electronic components of the kit are identified.
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</p>
</p>
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<p>
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<br><br>
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The software used in the platform is based on the <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Overview"> model</a> derived for the analysis of the fluorescence data obtained with the biosensor. We have also created a GUI that allows the students to modify the parameters used in the model and to visualize on a computer display the current/voltage output (which is the equivalent of the fluorescence output in our experiments).
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            </section>
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        </div>
 
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    <header id = "header">
 
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<h1 id = "section1-4">
 
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  Team presentations to groups of high school students
 
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</h1>
 
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        </header>
 
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        <div id="core" class="clearfix">
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            <section id="left">
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<b> Build a BioBrick </b>
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            <header id = "header2">
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<ol>
 +
<li> Insert the start-sequence, represented by the first set of 2-pin jumpers on the far left of the main unit. </li>
 +
<li>Select a promoter from the 4 provided, and insert each promoter region. </li>
 +
    <ul>
 +
    <li> A single promoter is composed of 3 promoter regions, represented by identically-colored resistors. </li>
 +
    <li> Note the orientation of the components when inserting each region. </li>
 +
    <li> The top resistor should connect slots 1 & 2. The middle resistor should connect slots 2 & 3. The bottom resistor should connect slots 3 & 4. </li>
 +
    </ul>
 +
<br>
 +
<li> Insert the tRNA stabilizer headers (2). </li>
 +
<li>  Insert the Spinach sequence (6-pin header). </li>
 +
<li>  Insert both RBS & FAP sequences. </li>
 +
<li>  Insert the end-sequence, represented by the final set of 2-pin jumpers.  </li>
 +
</ol>
 +
<br><br>
 +
 
 +
 
 +
 
 +
<b> Characterize the Chosen Promoter </b>
 +
<ol>
 +
<li> Open Matlab, and add the folder with the provided software to the Matlab path.</li>
 +
    <ul><li> Right click the provided folder, and select "Add to Path -> Selected Folders and Sub-Folders" </li></ul>
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<li> Type "BioBrick_GUI" at the command prompt, and hit enter. </li>
 +
<li> First, populate the time-step input table from top to bottom with the values 10, 20, 30, 40 ,50 </li>
 +
<li> Next, hit "Begin Time Lapse" at the top of the GUI: </li>
 +
    <ul>
 +
    <li> Note that the software will first sweep through the entire range of all possible fluorescence input levels, and plot the measured fluorescence values. </li>
 +
    <li> Allow the program to run to completion, populating the output tables. </li>
 +
    </ul>
 +
<br>
 +
<li>  When the program is finished populating the outputs, hit "Calculate" to display the output values for translational efficiency and transcriptional strength. </li>
 +
<li>  To export the output tables to the Matlab workspace, select "File" from the menu bar, and choose "Export".</li>
 +
    <ul><li> This will move the output tables, and calculated values to the workspace. </li></ul>
 +
<br>
 +
<li>  To plot an example comparison of the different promoters over time, enter "plot_data" at the Matlab command prompt. </li>
 +
    <ul><li> Observe the plot_data.m function if you wish to plot your own data </li></ul>
 +
</ol>
 +
<br><br>
 +
 
 +
 
 +
 
 +
<b> Make a Change and Observe the Effect! </b>
 +
<li> Any of the following changes can be made to the BioBrick to help demonstrate the component relationships: </li>
 +
    <ul>
 +
    <li> Remove the Spinach sequence, </li>
 +
    <li> Remove the tRNA stabilizer (one or both components), </li>
 +
    <li> Remove the RBS sequence, and replace with one of the 3-pin headers with blue wire (short), </li>
 +
    <li> Remove the FAP sequence, and replace with one of the 3-pin headers with blue wire (short), </li>
 +
    <li> Remove the START/END sequence, </li>
 +
    <li> Remove either DFHBI or MG by toggling the switches off (illuminated when 'ON'), </li>
 +
    <li> …or any combination of the previous. </li>
 +
    </ul>
 +
 
 +
<br><br>
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<h1 id="section1-1">Pictures and Schematics of the Kit </h1>
 +
 
 +
<b>BioBrick Circuit Kit</b><br>
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<img src="https://static.igem.org/mediawiki/2012/9/9a/CMU_BioBrick_Both_Units.jpg" height="300" width="433"/>
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<br><br>
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<b>BioBrick Components</b><br>
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<img src="https://static.igem.org/mediawiki/2012/1/16/CMU_BioBrick_Components.JPG" height="300" width="433"/>
 +
<br><br>
 +
 
 +
<b>BioBrick Main Unit Circuit Diagram</b><br>
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<img src="https://static.igem.org/mediawiki/2012/f/f3/CMU_Circ_Biobrick.png" height="300" width="700"/>
 +
<br><br>
 +
 
 +
<b>BioBrick Fluorescence Unit Diagram</b><br>
 +
<img src="https://static.igem.org/mediawiki/2012/a/a9/CMU_Circ_Fluor.png" height="300" width="433"/>
 +
<img src="https://static.igem.org/mediawiki/2012/a/a9/CMU_Circ_PhotoR.png" height="300" width="433"/>
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<br><br>
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<p>
<p>
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  </p>
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To download the more detailed schematic files for your own design, please follow this <a href="https://www.dropbox.com/sh/nb9cs0gpbvlrpxa/PMXNzM1p7G"> link</a>.
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</p>
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<p>
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To obtain feedback for how high school students use the circuit kit, the team has given several presentations about synthetic biology and our project to high school students enrolled in the Summer Academy of Math and Science and in AP Biology at Carnegie Mellon University. We have also sought and obtained feedback on the kit from a Physics teacher from a local Public School in Pittsburgh.  This feedback and input gained in these presentations is used to refine the kit.
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</p>
</p>
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         </div>
         </div>

Latest revision as of 04:01, 27 October 2012

Image:CMU_image6.jpeg




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.
Most importantly, we hope all iGEM teams can take inspiration from our experiences and build similar electric analogs of their BioBricks designs! We've found them to be an amazing tool for engaging high school students and piquing their interest and understanding in Synthetic Biology.

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.

Matlab BioBrick GUI 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
    1. Use the provided usb cable to connect the platform to a computer. Please do not detach the cable from the kit.
    2. The GUI is implemented in Matlab currently, but will also be implemented via an open-source language.
    3. 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
    1. Insert the start-sequence, represented by the first set of 2-pin jumpers on the far left of the main unit.
    2. 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.

    3. Insert the tRNA stabilizer headers (2).
    4. Insert the Spinach sequence (6-pin header).
    5. Insert both RBS & FAP sequences.
    6. Insert the end-sequence, represented by the final set of 2-pin jumpers.


    Characterize the Chosen Promoter
    1. 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"
    2. Type "BioBrick_GUI" at the command prompt, and hit enter.
    3. First, populate the time-step input table from top to bottom with the values 10, 20, 30, 40 ,50
    4. 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.

    5. When the program is finished populating the outputs, hit "Calculate" to display the output values for translational efficiency and transcriptional strength.
    6. 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.

    7. 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.


    Pictures and Schematics of the Kit

    BioBrick Circuit Kit


    BioBrick Components


    BioBrick Main Unit Circuit Diagram


    BioBrick Fluorescence Unit Diagram


    To download the more detailed schematic files for your own design, please follow this link.

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