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Team:Berkeley Software/Eugene Examples
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<span id="Examples"><H3>Examples</H3></span> | <span id="Examples"><H3>Examples</H3></span> | ||
Several Device constructs have been selected from the Registry of [http://partsregistry.org/ Standard Biological Parts] to show the creation of visual and textual designs. The visual representation has been implemented using [http://openwetware.org/wiki/Endy:Notebook/BioBrick_Open_Graphical_Language Visual BioBrick Open Language symbols] and [[Team:Berkeley_Software/Spectacles|Spectacles]], a visual tool editor, while Eugene was employed to demonstrate a textual representation. Due to the one to one relationship between standard biological parts and the Eugene syntax, the conversion could easily be achieved in both directions.<br><br> | Several Device constructs have been selected from the Registry of [http://partsregistry.org/ Standard Biological Parts] to show the creation of visual and textual designs. The visual representation has been implemented using [http://openwetware.org/wiki/Endy:Notebook/BioBrick_Open_Graphical_Language Visual BioBrick Open Language symbols] and [[Team:Berkeley_Software/Spectacles|Spectacles]], a visual tool editor, while Eugene was employed to demonstrate a textual representation. Due to the one to one relationship between standard biological parts and the Eugene syntax, the conversion could easily be achieved in both directions.<br><br> | ||
| - | [http://partsregistry.org/Part:BBa_K112809 BBa_K112809] is T4 Lysis Device with Pbad as the inducible Promoter. The Lysis device allows for the easy release of any product produced in the cell. The main file in Figure | + | [http://partsregistry.org/Part:BBa_K112809 BBa_K112809] is T4 Lysis Device with Pbad as the inducible Promoter. The Lysis device allows for the easy release of any product produced in the cell. The main file in Figure 1b displays the construct as an ordered list of Parts, while the header files are imported to hide the details of the Part declarations. With only one line of declaration, a complicated Device construct can be reproduced while the detailed information can still be accessed.<br><br> |
| - | <p align="center">'''Figure | + | <p align="center">'''Figure 1a: Visual representation of BBa_K112809'''</p> |
[[Image:Spectacles_screenshot_BBa_K112809.jpg|center]]<br> | [[Image:Spectacles_screenshot_BBa_K112809.jpg|center]]<br> | ||
| - | <p align="center">'''Figure | + | <p align="center">'''Figure 1b: Textual representation of BBa_K112809'''</p> |
[[Image:BBa_K112809Picture.png|900px|center]]<br><br> | [[Image:BBa_K112809Picture.png|900px|center]]<br><br> | ||
| - | [http://partsregistry.org/Part:BBa_E7104 BBa_E7104] is a GFP Reporter Device. Again, each new Device can be created using very few lines of code as Figure | + | [http://partsregistry.org/Part:BBa_E7104 BBa_E7104] is a GFP Reporter Device. Again, each new Device can be created using very few lines of code as Figure 2 demonstrates.<br><br> |
| - | <p align="center">'''Figure | + | <p align="center">'''Figure 2a: Visual representation of BBa_E7104'''</p> |
[[Image:Spectacles_screenshot_BBa_E7104.jpg|center]]<br> | [[Image:Spectacles_screenshot_BBa_E7104.jpg|center]]<br> | ||
| - | <p align="center">'''Figure | + | <p align="center">'''Figure 2b: Textual representation of BBa_E7104'''</p> |
[[Image:BBa_E7104Picture.png | center]]<br><br> | [[Image:BBa_E7104Picture.png | center]]<br><br> | ||
| - | [http://partsregistry.org/Part:BBa_K118021 BBa_K118021] in Figure | + | [http://partsregistry.org/Part:BBa_K118021 BBa_K118021] in Figure 3a is a Promoter characterization Device. The second Part in [http://partsregistry.org/Part:BBa_K118021 BBa_K118021] is a Reporter as specified by the [http://partsregistry.org/ Standard Registry of Parts]. It has no image associated, since technically speaking [http://partsregistry.org/Part:BBa_J33204 BBa_J33204] is a Device. However, currently with the available standards and specifications, there does not exist a way of breaking this Device cleanly into separate existing Parts. For example, there needs to be a way of specifying point mutation, which could be a feature of Devices, currently not supported by Eugene but is considered for future releases. Therefore, [http://partsregistry.org/Part:BBa_K118021 BBa_K118021] was specified as the Part Reporter rather than Device in the code.<br><br> |
| - | <p align="center">'''Figure | + | <p align="center">'''Figure 3a: Visual representation of BBa_K118021'''</p> |
[[Image:Spectacles_screenshot_BBa_K118021.jpg|center]]<br> | [[Image:Spectacles_screenshot_BBa_K118021.jpg|center]]<br> | ||
| - | <p align="center">'''Figure | + | <p align="center">'''Figure 3b: Textual representation of BBa_K118021'''</p> |
[[Image:BBa_K118021Picture.png|center]]<br><br> | [[Image:BBa_K118021Picture.png|center]]<br><br> | ||
| - | [http://partsregistry.org/Part:BBa_I8510 BBa_I8510] in Figure | + | [http://partsregistry.org/Part:BBa_I8510 BBa_I8510] in Figure 4a is an Inverter that takes 3OC6HSL as input and produces lacZalpha as output. It also creates an orthogonal GFP protein generator.<br><br> |
| - | <p align="center">'''Figure | + | <p align="center">'''Figure 4a: Visual representation of BBa_I8510'''</p> |
[[Image:Spectacles_screenshot_BBa_I8510.jpg|center]]<br> | [[Image:Spectacles_screenshot_BBa_I8510.jpg|center]]<br> | ||
| - | <p align="center">'''Figure | + | <p align="center">'''Figure 4b: Textual representation of BBa_I8510'''</p> |
[[Image:BBa_I8510Picture.png|center]]<br><br> | [[Image:BBa_I8510Picture.png|center]]<br><br> | ||
<html> | <html> | ||
<center> | <center> | ||
| - | <caption> | + | <caption>Here we provide a brief flash demo which illustrates the Eugene design process.</caption> |
<embed | <embed | ||
src="https://static.igem.org/mediawiki/2009/7/72/BerkeleySoftware_EugeneWink.swf" | src="https://static.igem.org/mediawiki/2009/7/72/BerkeleySoftware_EugeneWink.swf" | ||
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<br><br> | <br><br> | ||
| - | <p style="text-align: right;">[[# | + | <p style="text-align: right;">[[#Examples|Back Up]]</p> |
Latest revision as of 23:03, 21 October 2009
Examples
Several Device constructs have been selected from the Registry of [http://partsregistry.org/ Standard Biological Parts] to show the creation of visual and textual designs. The visual representation has been implemented using [http://openwetware.org/wiki/Endy:Notebook/BioBrick_Open_Graphical_Language Visual BioBrick Open Language symbols] and Spectacles, a visual tool editor, while Eugene was employed to demonstrate a textual representation. Due to the one to one relationship between standard biological parts and the Eugene syntax, the conversion could easily be achieved in both directions.
[http://partsregistry.org/Part:BBa_K112809 BBa_K112809] is T4 Lysis Device with Pbad as the inducible Promoter. The Lysis device allows for the easy release of any product produced in the cell. The main file in Figure 1b displays the construct as an ordered list of Parts, while the header files are imported to hide the details of the Part declarations. With only one line of declaration, a complicated Device construct can be reproduced while the detailed information can still be accessed.
Figure 1a: Visual representation of BBa_K112809
Figure 1b: Textual representation of BBa_K112809
[http://partsregistry.org/Part:BBa_E7104 BBa_E7104] is a GFP Reporter Device. Again, each new Device can be created using very few lines of code as Figure 2 demonstrates.
Figure 2a: Visual representation of BBa_E7104
Figure 2b: Textual representation of BBa_E7104
[http://partsregistry.org/Part:BBa_K118021 BBa_K118021] in Figure 3a is a Promoter characterization Device. The second Part in [http://partsregistry.org/Part:BBa_K118021 BBa_K118021] is a Reporter as specified by the [http://partsregistry.org/ Standard Registry of Parts]. It has no image associated, since technically speaking [http://partsregistry.org/Part:BBa_J33204 BBa_J33204] is a Device. However, currently with the available standards and specifications, there does not exist a way of breaking this Device cleanly into separate existing Parts. For example, there needs to be a way of specifying point mutation, which could be a feature of Devices, currently not supported by Eugene but is considered for future releases. Therefore, [http://partsregistry.org/Part:BBa_K118021 BBa_K118021] was specified as the Part Reporter rather than Device in the code.
Figure 3a: Visual representation of BBa_K118021
Figure 3b: Textual representation of BBa_K118021
[http://partsregistry.org/Part:BBa_I8510 BBa_I8510] in Figure 4a is an Inverter that takes 3OC6HSL as input and produces lacZalpha as output. It also creates an orthogonal GFP protein generator.
Figure 4a: Visual representation of BBa_I8510
Figure 4b: Textual representation of BBa_I8510
