Team:Johns Hopkins-Software/AutoDesign

From 2012.igem.org

AutoDesign

AutoGene was developed to make a simple-to-use design tool whereby users can select features they want to design with, drag these features into the order they want, perform operations on these features, and then import their newly designed plasmid to the workspace.

A user starts by selecting features they want to design with. These features can be chosen from multiple plasmids in the workspace. To select a feature, a user simply drags that annotation into the Design Registry, a listing of features the user wants to save for later use. We wanted to make this process extremely intuitive and easy, so we implemented a user-friendly drag and drop system whereby a user can drag their cursor over multiple features from a plasmid and drag them into the design registry all at once. They pop inside the pane on the right side of the screen, waiting to be designed with

When a user is ready to begin designing, they continue the drag and drop process by dragging features from the private registry into the design pane. The whole process is especially user-friendly and simple to use. Anyone can use it, and this was also another one of our major goals. The design pane consists of three windows which are discussed below. As the plasmid is made, the associated DNA sequence and the associated picture of the plasmid is updated in real time so that a user can get a real view into the Plasmid they are designing. AutoPlasmid helps visualize this new plasmid. Once a plasmid is done being designed, the user may import it into the workspace and then export as a genbank, fasta, and SBOL as discussed above

Interface Organization


Design Pane. The user drags features from the Private Registry into the Design Pane. Each feature type has an associated icon (ex. a Terminator is a capital T). The user may user the design pane to rearrange features using an easy drag and drop process. They may also right click any feature to perform a number of operators on that feature, such as duplicate, delete, and invert.

DNA Pane. The DNA Pane shows the current DNA that is contained inside the plasmid that is being designed. Different features are highlighted in different colors associated with their feature type. For example, Origins are in brown. The DNA updates as the user continues to design their plasmid in the Design Pane.

PlasmidView. The PlasmidView shows the current Plasmid, and is updated just as the DNA Pane is updated while the user designs their plasmid.



How to use AutoDesign

Using the annotated features that AutoPlasmid finds, the user may select features to design a new plasmid with. First, the user chooses features and drags them into the private registry.



Next, the user drags features into the private registry. The user can change the order of features, invert features, duplicate features, and delete features. At the same time, the user sees an updated version of the plasmid they are designing and the associated DNA.




































































































































































































































Autogene

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