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CREATING AND IMPORTING DESIGNS
CREATING AND IMPORTING DESIGNS

A design is a schematic representation of a DNA assembly process in which users specify the biological parts in the final construct.

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Written by Daniela Alvarez
Updated yesterday

CONTENTS OF THIS ARTICLE


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.


CREATING A 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 click "Save". This will take you to the Design editor. There, you can see a blank design with two bins with no more information.

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 the “Choose File” button and select the file with your design. Supported format: JSON. Click Save.


LOADING EXAMPLE DESIGNS

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. To load an example design, follow the same procedure explained above, but this time select the assembly method you want to use.

The image below is an example of a Combinatorial Golden Gate design.


WORKING WITH DESIGNS

When working on the design Editor, there are several options you can change:

  • Add bins or rows: You can add a new part by adding a new bin, or add a variant of a part by adding a new row (this can only be done with a combinatorial design). Remember that this can be done by clicking on the "plus (+)" icon.

  • Assign a DNA part to a bin: You can associate one DNA part or more (if it's combinatorial) to a bin. To do this, double-click on the empty cell under the bin and a window will be displayed, where you can select the DNA part(s) you want to associate.

  • View and edit a bin's properties: Click on a bin to open the side panel with its information. There, you can change its name, direction, overhang position, change the design rulesets, and add/remove an specific number of basepairs from the 3' or 5' endings.


    To change the SBOL icon of a bin, click on the icon shown on the side panel and select an icon from the list.

  • View and edit a part's properties: Similar to the side panel shown when clicking on a bin, you can also obtain and edit information by clicking on a part associated (cells under each bin). This will show a side panel where you can add notes on the part, indicate your preferred overhangs, and indicate forced assembly strategies.

  • Forced Assembly Strategy: When editing the information of a part, you can indicate the forced assembly strategy by selecting from the list

    Once you do this, the software will show a small colored square on the left upper corner of a part; you can obtain information about it by placing the cursor over it.

  • Notice duplicated parts: TeselaGen's software automatically detects duplicated parts and warns you by showing a yellow frame on the duplicated parts.

  • Add a direct synthesis firewall: One of the options shown in the side panel of a part allows you to add a direct synthesis firewall. In this case, you will be notified with a red frame shown on the corresponding part.


ANALYZING A DESIGN

Once your design is ready, you can use one of TeselaGen's most powerful tools by clicking on the "Submit for Assembly" option in the right upper corner of your screen.

You can check the status of your report on the notifications icon. In some cases, there are assembly errors, where the software will indicate the changes you need to do to successfully run the assembly analysis.


On the other hand, if the assembly successfully runs with no errors, you can access to it on the corresponding notification:

Another way to access the report is through the DNA Assembly Reports library:

A report contain the following sections:

  • Prebuilt constructs. These include the desired sequences that were already built and are available on the physical inventory.

  • Constructs. Final desired sequences to be built using the Design analysis.

  • Input sequences. Obtained from the input parts.

  • Input parts used in the analysis.

  • Assembly oligos that need to be synthesized.

  • Annealed oligos.

  • Digest linearized fragments that are going to be used in the assembly reaction.

  • Synthon sequences. Includes the sequences that need to be directly synthesized.

  • PCRs need to be run to generate the assembly pieces.

  • Assembly Pieces of DNA that will be in the final assembly reaction.

  • Assemblies. Includes assembly pieces that need to be combined to create each construct.

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