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Assembly Reaction Planning Tool
Assembly Reaction Planning Tool
Written by Chris Lamkin
Updated over a week ago

This tool takes in a list of constructs you would like to assemble, as well as the plate(s) containing the materials necessary to create those constructs. It outputs a worklist and reaction map specifying how those materials need to be combined to create the constructs.

Input: Construct List and Source Plate

Output: Worklist, Reaction Map, Destination Plates

You can find more detailed definitions of the terms mentioned in this article in the glossary.

You can find the Assembly Reaction Planning tool under Tools > Tool Library. Click on ‘Launch Tool’ to start using the tool.

The tool will walk you through several steps. You need to complete each step before proceeding to the next. After completing a step, the completed step mark (circle) will turn green with a checkmark. You can always use the ‘previous’ button to go back to any previous step.

  1. Select j5 Construct List: In this first step, you will select your constructs and source plates or tubes. Clicking on 'Select Construct Lists' will bring you to a dialog where you can select from available construct lists. Construct lists can be created via the DNA Assembly Construct Selection Tool. In this example, we are choosing the standard Combinatorial Golden Gate example list.

After this step, you should see the constructs listed as shown below. The standard Combinatorial Golden Gate example has eight constructs.

Now, we 'Select Plates'. The Select Plates dialog shows several plates in inventory, only one of which is relevant to our Golden Gate example. Let's select that plate and continue.

The selected plate is now shown. Click on the 'eye' icon to take a closer look.

You will receive an error message if the selected plates or tubes are missing any necessary materials and will have to address these issues before continuing.

2. Destination Plate Configuration: The second step contains many options for configuring the destination plate(s) for assembly reactions.

Here you will be able to select a specific plate type and specify a row or column first layout for the reactions. For more advanced layouts, select a custom plate map to dictate destination plate layout. These can be created via the Create Plate Map Tool, and should contain the constructs selected in Step 1. You will also be prompted to provide transfer volume information for the output worklist.

3. Review Reaction Plans: In the final step, you will be able to provide names for the output Worklist and Reaction Map, and can preview the worklist before completing the tool.

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