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Team:Carnegie Mellon/Hum-Software
From 2012.igem.org
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| - | <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom- | + | <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Attributions">Attributions</a> |
| + | </li> | ||
| + | <li> | ||
| + | <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hom-Acknowledgements">Acknowledgements</a> | ||
</li> | </li> | ||
</ul> | </ul> | ||
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Bio-Submitted">Submitted Parts</a> | <a href="https://2012.igem.org/Team:Carnegie_Mellon/Bio-Submitted">Submitted Parts</a> | ||
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</ul> | </ul> | ||
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Notebook">Notebook</a> | <a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Notebook">Notebook</a> | ||
| + | </li> | ||
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| + | <a href="https://2012.igem.org/Team:Carnegie_Mellon/Met-Safety">Safety</a> | ||
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</ul> | </ul> | ||
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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> | ||
| + | </li> | ||
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| + | <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Expanded">Expanded</a> | ||
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</ul> | </ul> | ||
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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> | ||
<ul> | <ul> | ||
| - | <li class = 'offset' style ='width: | + | <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> | ||
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<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Outreach">Outreach</a> | <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Outreach">Outreach</a> | ||
</li> | </li> | ||
| - | <li | + | <li> |
<a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Circuit">Circuit Kit</a> | <a href="https://2012.igem.org/Team:Carnegie_Mellon/Hum-Circuit">Circuit Kit</a> | ||
| - | + | </li> | |
| - | + | <li class="current"> | |
| - | + | <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> | ||
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</ul> | </ul> | ||
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<br /><br /><br /> | <br /><br /><br /> | ||
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<!--Main Contents --> | <!--Main Contents --> | ||
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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 here. | + | We implemented the model described <a href="https://2012.igem.org/Team:Carnegie_Mellon/Mod-Matlab"> here</a>. |
</p> | </p> | ||
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<header id = "header"> | <header id = "header"> | ||
<h1 id = "section1-2"> | <h1 id = "section1-2"> | ||
| - | GUI | + | BioBrick Circuit GUI |
</h1> | </h1> | ||
</header> | </header> | ||
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| - | 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 | + | 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 |
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| + | <img src="https://static.igem.org/mediawiki/2012/4/4d/CMU_BioBrick_GUI_Screen_Shot.png" height="400" width="405" align="right"/> | ||
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| + | 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> | ||
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<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 computational function that implements the model, 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
The software consists of two parts: model implementation and GUI, both written in Matlab.
Physical Model
We implemented the model described here.
BioBrick Circuit GUI
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.
