Auto-generate parts from a set of j5 input files
This functionality allows you to generate (a starting point for) a DeviceEditor design from a set of j5 input files. This is useful if you have the complete set of files required for designing a DNA assembly protocol with j5, but either you no longer have the corresponding DeviceEditor saved design .xml file, or you generated the j5 input files without using DeviceEditor (e.g. using a spreadsheet program).

Demonstration video:

Here is a demonstration video that goes through this process (Load design from j5 files.mov, right click this link to save the movie to disk for better viewing):

Here is a zip file (containing the j5 input files) that you can use as a starting point for reproducing the demonstration above (SLIC_Gibson_CPEC_example12.
Here is a DeviceEditor .xml saved design file resulting from saving after the demonstration above (Load design from j5 files.xml, right click and save link as to save the design file to disk):


You can auto-generate a DeviceEditor design from j5 input files by going to the "File" menu at the top left of the DeviceEditor display, and clicking on "Load Design". At this point you'll have three options, and in this example we'll click on "j5 Files" (another option, loading a design from "Design XML", is discussed in a previous section). Auto-generating a design entails first clearing the current canvas, so a warning message will pop-up telling you that you're about to clear the current design and any unsaved changes will be lost. If you really want to clear the current design and load another, click "Ok"; conversely, clicking "Cancel" won't clear the current design nor load a new one. After clicking "Ok", a new "j5 File Import" dialog box will pop-up.

There are four j5 input files that will need to be imported: the "Sequence List file", "zipped sequence files", "Part List file", and "Target Part Order file". For more information on these files, please see the j5 input files documentation. For each of these files, you'll click the corresponding "Import ..." button, which will pop-up a "Select file to upload" dialog box, allowing you to select the file you'd like to import. For the "Sequence List file", "Part List file", and "Target Part Order file", only files with .csv extensions will be selectable. For the "zipped sequence files", only files with .zip extensions will be selectable. Once a file is successfully imported, the file status will go from red "Not ready", to green "Ready". At any time during this process, you can click the "Clear Imports" button, which will reset all of the files to be imported. Once all of the four files are "Ready", you can click "Done" to complete the process.

Note that DeviceEditor designs utilize slightly more information than can be reconstituted from j5 input files alone. For example, the optional SBOL Visual icons associated with collection columns in DeviceEditor is not captured in the j5 input files, so by default, all of the columns will be associated with the generic SBOL Visual icon, but it is a simple procedure to change the SBOL Visual icon associated with a column.

Also note that the Eugene design specification rules are not imported during this process. To do this, you may subsequently import a Eugene rules file, or create the Eugene design rules from scratch.