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Team:BostonU/Clotho
From 2013.igem.org
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<p>Our project is focused on creating a standardized method for the characterization of genetic circuits in synthetic biology. In order to achieve this goal, it is necessary to have a platform that enables us to create the standardized data, organize it and manage it efficiently. <a href="http://clothocad.org" style="color:#B22222; display:inline;">Clotho</a> is a great synthetic biology tool that has been helping us with exactly that! | <p>Our project is focused on creating a standardized method for the characterization of genetic circuits in synthetic biology. In order to achieve this goal, it is necessary to have a platform that enables us to create the standardized data, organize it and manage it efficiently. <a href="http://clothocad.org" style="color:#B22222; display:inline;">Clotho</a> is a great synthetic biology tool that has been helping us with exactly that! | ||
</p> | </p> | ||
| - | <p>This section aims to describe how we have been using Clotho in our project. We divided the content into the <h10><a href="http://wiki.bu.edu/ece-clotho/index.php/App_Information" style="color:#B22222; display:inline | + | <p>This section aims to describe how we have been using Clotho in our project. We divided the content into the <h10><a href="http://wiki.bu.edu/ece-clotho/index.php/App_Information" style="color:#B22222; display:inline;>Clotho Apps</a></h10> we used, giving a brief explanation of how each App works and examples of situations in which they were useful for our project. |
We hope you can all get good ideas on how to use Clotho on your projects and take advantage of this amazing tool!</p> | We hope you can all get good ideas on how to use Clotho on your projects and take advantage of this amazing tool!</p> | ||
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Revision as of 18:53, 22 July 2013
Clotho and Eugene
Our project is focused on creating a standardized method for the characterization of genetic circuits in synthetic biology. In order to achieve this goal, it is necessary to have a platform that enables us to create the standardized data, organize it and manage it efficiently. Clotho is a great synthetic biology tool that has been helping us with exactly that!
This section aims to describe how we have been using Clotho in our project. We divided the content into the
Also, the description section helps to give meaning to the nickname and makes the inventory more user-friendly. Sequence Viewer is a very useful app to analyze sequences that are in the inventory . It allows us not only to view the sequences of DNA, but also to interact with it by highlighting specific portions that we are interested in. For example, we used sequence viewer to find and highlight restriction and fusion sites within the sequence.
In this example above, we are defining our basic parts. Although the fusion/MoClo sites themselves are not basic parts, we consider them as a separate entities because they are essential when combining different MoClo parts. At this point, fusion sites as a separate part would be a more versatile method of using the language.
After defining which parts Eugene will be combining to together, the next step would be to identify the device. In this case, different basic parts are combined to form a moclo level 0 part.
After defining our MoClo level 0 devices, the next step is to define level MoClo Level 1 devices. In this case, a level 1 device is designated to include a promotor, rbs, gene and terminator. Additional rules are added as needed. For instance, we are creating rules to make sure the Moclo sites of subsequent parts are the same so they are able to be ligated together. In the picture the rule is expressed for Promoter and RBS. Also, we have to be consistent with the design of the MoClo parts, it means that the part can`t be flanked by the same MoClo sites as show in the second rule.
