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.

Blasto

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

Eugene, a language based on Java, 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.

The BostonU iGEM team used Eugene to determine the number of permutations for transcriptional units that can be assembled from the MoClo parts and devices specified by the user. To eliminate extraneous permutations, the user must specify rules pertaining to the order and relationship between parts. Eugene can be utilized via Clotho's Eugene Scriptor app.

To write a Eugene script, one must first declare the parts that are being used and their properties. Next, one must define the specific properties for each part. To define the devices, structural rules must be made defining what parts are in each device. Content rules describe the relationships between parts. Lastly, the user can compute permutations and print out the results.

Below is an example of a Eugene script for a generic quorum sensing circuit.

PigeonCAD

PigeonCAD is a very useful tool for synthetic biology because it allows the user to visualize genetic devices. Using the Synthetic Biology Open Language (SBOL) and a simple code, the user can easily build a circuit (Bhatia et al., 2013). We used Pigeon to depict our genetic circuits.

Depicted below is an example of a simple transcriptional unit depicted in SBOL with the corresponding Pigeon code.




The PigeonCAD website has additional examples.

References

[1] Xia, B., Bhatia, S., Bubenheim, B., Dadgar, M., Densmore, D., and Anderson, J.C. (2011) "Clotho: A Software Platform for the Creation of Synthetic Biological Systems, A Developer’s and User’s Guide for Clotho v2.0." Methods in Enzymology 498:97-135. doi: 10.1016/B978-0-12-385120-8.00005-X.
[2] Bilitchenko, L., Liu, A., Cheung, S., Weeding, E., Xia, B., Leguia, M., Anderson, J.C., and Densmore, D. (2011) "Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems." PLoS ONE 6(4): e18882. doi:10.1371/journal.pone.0018882.
[3] Bhatia, S., and Densmore, D. (2013) "Pigeon: A Design Visualizer for Synthetic Biology." ACS Synthetic Biology 2(6):348–350. doi: 10.1021/sb400024s.