Team:BostonU/Clotho

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. We have been utilizing Clotho, a synthetic biology software suite developed with tools for analyzing and organizing data.

This section aims to describe how we have been using Clotho in our project. We divided the content into the Clotho Apps 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!

Blasto can be used to verify DNA sequences by comparing a sequence with the expected sequence. Blasto shows the percentage of the match and the number of gaps between sequences and where those gaps occur. Users can create a collection of their parts and save sequences for easy comparison.

Eugene is a language based off of Java which is both human and machine readable. Currently the language can be used to expedite the design process for new devices by providing a list of possible transcriptional units based on specific rules and parts available.

Still in its beta stages, the BU iGEM team used Eugene to come up with a list of possible transcriptional units that could be assembled from the MoClo parts we made for each project. By specifying rules concerning fusion sites and restriction sites, we let Eugene do the designing for us, while we then selectively choose which transcriptional units to create. Below is a sample of Eugene script.

We were fortunate to be able to use Eugene through Clotho's Eugene Scriptor. The first task in writing a Eugene script is to define what the parts are. Notice that the language is very straightforward and intuitive.

In the 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 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 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 below, the rule is expressed for promoter and RBS. Additionally, we have to be consistent with the design of the MoClo parts, which means that the part can not be flanked by the same MoClo sites as shown in the second rule.