28 Creating sequence files (from mapped parts) and j5 input files After mapping a sequence to a part, it is possible to have DeviceEditor reconstitute the Genbank, FASTA, or jbei-seq (JBEI Registry/VectorEditor) format sequence file to which the part is mapped. In addition, once the design collection is "j5 ready", we can create a set of input files for j5. (Note: to be "j5 Ready", each collection column must contain at least one mapped part). We can also create a j5 parameters input file (for example, after we have modified the j5 parameters) or a downstream automation parameters input file (for example, after we have modified the downstream automation parameters). Demonstration video: Here is a demonstration video that goes through this process (Create j5 input files.mov, right click this link to save the movie to disk for better viewing): Here is a DeviceEditor .xml saved design file that you use as a starting point for reproducing the demonstration above (SLIC_Gibson_CPEC_example.xml, right click and save link as to save the design file to disk): Here is the Genbank format sequence file resulting from the demonstration above (pBbS8c-RFP.gb): Here is the zip file (containing the generated j5 input files) resulting from the demonstration above (SLIC_Gibson_CPEC_example12.5.27.2.30.52_completeOutput.zip): Here is the j5 parameters .csv file resulting from the demonstration above (j5_parameters.csv, right click and save link as to save the parameters file to disk): Here is the downstream automation parameters .csv file resulting from the demonstration above (downstream_automation_parameters.csv, right click and save link as to save the parameters file to disk): Narrative: Generating sequence files from mapped parts: With a mapped part selected (active) in the design canvas, it is possible to re-generate a sequence file (for the part's source) that can be saved to disk. Click the "j5" button at the top left of the DeviceEditor display. This will pop-up a new  "j5 Controls" dialog box. Within this dialog box, click on the "j5 Files" tab. Within this tab, you will have one of three relevant options available (non grayed-out): "Genbank File Create", or "FASTA File Create", or "jbei-seq File Create" depending on if the part was originally mapped from a Genbank, FASTA, or jbei-seq format sequence file. Clicking on the appropriate button will pop-up a new "Select location for download" dialog, which will allow you to save the file to your desired location. Generating a set of j5 input files from a "j5 Ready" collection object: For more information on the various j5 input files, refer to the "j5 input files" section in the j5 user's manual. (Note: to be "j5 Ready", each collection column must contain at least one mapped part icon). With the "j5 Ready" status indicator a green "True" in the panel on the right side of the DeviceEditor display within the "Collection Info" tab, it is possible to generate a set of input files for j5 that can be saved to disk. Click the "j5" button at the top left of the DeviceEditor display. This will pop-up a new  "j5 Controls" dialog box. Within this dialog box, click on the "j5 Files" tab. Within this tab, you will have several relevant options available (non grayed-out): "j5 Sequence File Generate", "j5 Parts File Generate", "j5 Target Parts File Generate", "j5 Eugene Rules File Generate", and "Download". Clicking one of these buttons will pop-up a new "Select location for download" dialog, which will allow you to save the corresponding file to your desired location. It is recommended to click the "Download" button option, as this will download the complete set of j5 input files together in a single zip file (as is done in the example demonstration video above). This zip file which contains all of the j5 input files is named based on a time stamp (e.g. "10.12.26.20.55.8", for December 26, 2010 at 8:55PM). Generating a j5 parameters input file: For more information the j5 parameters input file, refer to the "j5 parameters file" page in the j5 user's manual. Click the "j5" button at the top left of the DeviceEditor display. This will pop-up a new  "j5 Controls" dialog box. Within this dialog box, click on the "j5 Files" tab. Within this tab, click on the "j5 Parameters Generate" button, which will pop-up a new "Select location for download" dialog box, enabling you to choose where you'd like to save the parameters file to. Generating a downstream automation parameters input file: For more information the downstream automation parameters input file, refer to the "Downstream automation parameters file" page in the j5 user's manual. Click the "j5" button at the top left of the DeviceEditor display. This will pop-up a new  "j5 Controls" dialog box. Within this dialog box, click on the "j5 Files" tab. Within this tab, click on the "Downstream Automation Parameters Generate" button, which will pop-up a new "Select location for download" dialog box, enabling you to choose where you'd like to save the parameters file to.