Team:Carnegie Mellon/Hum-Software

From 2012.igem.org

(Difference between revisions)
 
(28 intermediate revisions not shown)
Line 16: Line 16:
<li>
<li>
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Team">Team</a>
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Team">Team</a>
 +
</li>
 +
<li>
 +
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Attributions">Attributions</a>
</li>
</li>
<li>
<li>
Line 72: Line 75:
<li>
<li>
<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>
 +
</li>
 +
<li>
 +
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Expanded">Expanded</a>
</li>
</li>
</ul>
</ul>
Line 79: Line 85:
<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>
<ul>
<ul>
-
<li class = 'offset' style ='width: 611px'> <a href="#"></a></li>
+
<li class = 'offset' style ='width: 295px'> <a href="#"></a></li>
<li>
<li>
<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>
Line 91: Line 97:
<li class="current">
<li class="current">
<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>
 +
</li>
 +
<li>
 +
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Team">Team Presentation</a>
 +
</li>
 +
<li>
 +
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Teaching">Teaching Presentation</a>
</li>
</li>
</ul>
</ul>
Line 96: Line 108:
</ul>
</ul>
     <br /><br /><br />
     <br /><br /><br />
 +
<!--Main Contents -->
<!--Main Contents -->
Line 130: Line 143:
                 The software consists of two parts: model implementation and GUI, both written in Matlab.  
                 The software consists of two parts: model implementation and GUI, both written in Matlab.  
                 </p>
                 </p>
-
                     <h1 id="section1-1"> Model</h1>
+
                     <h1 id="section1-1"> Physical Model</h1>
<p>
<p>
We implemented the model described <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Matlab"> here</a>.
We implemented the model described <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Matlab"> here</a>.
Line 142: Line 155:
     <header id = "header">
     <header id = "header">
<h1 id = "section1-2">
<h1 id = "section1-2">
-
   GUI
+
   BioBrick Circuit GUI
</h1>
</h1>
         </header>
         </header>
Line 151: Line 164:
     <p>
     <p>
-
The interface allows users to enter time-step data (e.g., at what time points should images be captured), which populates two tables, displayed in the GUI. When the user starts the time lapse, a full sweep of measured vs. actual fluorescence is plotted for both mRNA and protein. The GUI then iterates through each time-step, plotting a horizontal line with each sweep plot corresponding to the measured fluorescence at that particular time step. The GUI also populates both tables with the actual values as it moves to each next time step.
+
The interface allows users to enter time-step data (e.g., at what time points should images be captured), which populates two tables, displayed in the Matlab GUI. When the user starts the simulated microscopy time lapse, a full sweep of measured vs. actual fluorescence values are plotted for both mRNA and protein. This is essentially plotting the
 +
 
 +
<img src="https://static.igem.org/mediawiki/2012/4/4d/CMU_BioBrick_GUI_Screen_Shot.png" height="400" width="405" align="right"/>
 +
 
 +
quantity of light produced by the LEDs (representing cells) versus the quantity of light detected by the photo-resistor (representing the microscopy). The GUI then iterates through each time-step, plotting a horizontal line with each sweep plot corresponding to the measured fluorescence at that particular time step. The GUI also populates both tables with the actual values as it moves to each next time step.
</p>
</p>
 +
 +
  <p>
  <p>
-
Furthermore, the GUI successfully displays a relevant image of the cells at every timestep. Illuminated fields above the plots indicate which type of fluorescence (mRNA or protein) is currently being populated. When the time lapse is finished, a push-button becomes available which, when clicked, opens a dialog-box displaying and transcriptional strength (Ts) and translational efficiency (Tl). This component calls the <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Matlab"> computational function</a> that implements the <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Derivations"> model</a>, which computes Ts and Tl.
+
Furthermore, the GUI successfully displays a relevant image of the cells at every timestep. Illuminated fields above the plots indicate which type of fluorescence (mRNA or protein) is currently being populated. When the time lapse is finished, a push-button becomes available which, when clicked, opens a dialog-box displaying and transcriptional strength (<i>Ts</i>) and translational efficiency (<i>Tl</i>). This component calls the <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Matlab"> computational function</a> that implements the <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Derivations"> model</a>, which computes <i>Ts</i> and <i>Tl</i>.
</p>
</p>
<p>
<p>
  Finally, a File-Menu dropdown option ('Export') serves to export the table data for both mRNA and protein, as well as the computed values for transcriptional strength and translational efficiency to the local Matlab workspace.
  Finally, a File-Menu dropdown option ('Export') serves to export the table data for both mRNA and protein, as well as the computed values for transcriptional strength and translational efficiency to the local Matlab workspace.
</p>
</p>
 +
To download the software accompanying the kit, please visit the circuit kit <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Circuit"> documentation</a>, and scroll down to "General Notes" under the "Using the Hardware/Software Platform" section.

Latest revision as of 03:39, 27 October 2012

Image:CMU_image6.jpeg




The software consists of two parts: model implementation and GUI, both written in Matlab.

Physical Model

We implemented the model described here.

The interface allows users to enter time-step data (e.g., at what time points should images be captured), which populates two tables, displayed in the Matlab GUI. When the user starts the simulated microscopy time lapse, a full sweep of measured vs. actual fluorescence values are plotted for both mRNA and protein. This is essentially plotting the quantity of light produced by the LEDs (representing cells) versus the quantity of light detected by the photo-resistor (representing the microscopy). The GUI then iterates through each time-step, plotting a horizontal line with each sweep plot corresponding to the measured fluorescence at that particular time step. The GUI also populates both tables with the actual values as it moves to each next time step.

Furthermore, the GUI successfully displays a relevant image of the cells at every timestep. Illuminated fields above the plots indicate which type of fluorescence (mRNA or protein) is currently being populated. When the time lapse is finished, a push-button becomes available which, when clicked, opens a dialog-box displaying and transcriptional strength (Ts) and translational efficiency (Tl). This component calls the computational function that implements the model, which computes Ts and Tl.

Finally, a File-Menu dropdown option ('Export') serves to export the table data for both mRNA and protein, as well as the computed values for transcriptional strength and translational efficiency to the local Matlab workspace.

To download the software accompanying the kit, please visit the circuit kit documentation, and scroll down to "General Notes" under the "Using the Hardware/Software Platform" section.

Image:TartanFooter.jpeg