A design is a schematic representation of a DNA assembly process in which users specify the biological parts and the order they appear in the final assembled construct. Our Design Module allows you to create a design or import an existing design (JSON file format).
From the header, click on “Designs” and choose the submenu “Designs”. This opens the Design Library which is a repository of designs that you have created or imported.
New Design: To create or import a design, click on the green “New Design” button. At the “Create New Design” page you have the following options: create a new design, upload an existing design, or load an example design.
Create a new design: Give your design a name (this is required), you can add a description and you have the option to add the design to a Project, then just click Save. This will take you to the Design editor.
To upload a design file from your computer: Give your design a name, you can add a description and add the design to a Project if you want to, then click on “Choose File” button and select the file with your design. Supported format: JSON. Click Save.
Load in one of the example designs: Give your design a name, you can add a description and add the design to a Project if you want to, then choose from the dropdown menu at the bottom one of the five example designs available: Gibson, Golden Gate, Combinatorial Gibson, Combinatorial Golden Gate, Gateway. You can read more about these assembly methods in this article. Click Save.
If you upload a design or load in one of the example designs, the Design editor will be loaded with parts that are defined in the uploaded design or the example design.
We will talk about the Design editor in depth in another article. You can also take a look at one of our tutorial examples showing how we create a Design Library of DNA constructs using the design editor.
New DAPPER Design: This is a tool that accommodates the need to create a Design from an Alignment of Parallel Parts that Expose Regions of Diversity (DAPPER). When the “New DAPPER Design” button is clicked, a dialog will pop up and ask you to name the design and upload a file containing names and sequences in the alignment. The supported file formats currently are .tsv or .txt. If you want to know how these sequences and names appear in the file, you can download an example file by clicking Download Example File.
Once you upload a file, click Next. This will open a window in which the sequence alignment is shown.
The sequences are nearly identical but there are a few regions at which they differ from each other. These regions are highlighted in red. In the example above, there are three regions in which the sequences have base pairs different from one another. To create diversity region, select the highlighted region (click and drag) then right click and press “Create Diversity Region”. Users must do this step for all regions highlighted in red as shown in the navigating window below the sequences. Once all diversity regions have been created, click “Create Design”. The DAPPER design creates DNA parts from these diversity regions as well as identical regions and populates them as parts in the Design Editor. Parts of the same name represent identical regions, and parts with different names represent the variability of the diversity regions. We will talk about the Design Editor in more detail in another article . You just need to keep in mind that the DAPPER Design functionality gives users a convenient way to generate DNA parts from an alignment.
Loading Example Designs