Running a downstream automation design on the j5 server
At any time, we can use DeviceEditor to directly design a downstream automation process on the j5 server.
Here is a demonstration video that goes through this process (Run Downstream automation design.mov, right click this link to save the movie to disk for better viewing):
You'll also need the following files to exactly reproduce the demonstration above: Source plate list file (plate_list.csv): Zipped source plate files file (zipped_plates.zip): j5 assembly file (myassemblyfilelist_condensed.csv):
Here is a representative zip file resulting from this particular distribute PCR reactions example (j5_njhillson_20120527033014.zip):
For more information on designing downstream automation processes with j5, refer to the "Distribution of PCR reactions" 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 "Downstream Automation" tab. Within this tab, you will have two options available for the "Downstream Automation Parameters File": either "Use lastest server version" (which will use your most recently updated set of downstream automation parameters currently stored on the j5 server) or "Generate file from parameters" (which will generate the downstream automation parameters file on-the-fly, based on how you set the downstream automation parameters).Within this tab, there will be a "Choose File" button for "Source Plate List", "Zipped Plate Files", and "j5 Assembly File". For the "Source Plate List" and "j5 Assembly File" files, only files with .csv extensions will be selectable. For the "Zipped Plate Files", only files with .zip extensions will be selectable. Clicking on these buttons will pop-up a new "Select file to upload" dialog, for you to select which file you'd like to use. After you selected a file to upload for "Source Plate List", "Zipped Plate Files", and "j5 Assembly File", click the "Distribute PCR Reactions" button to initiate the process on the j5 server. After doing this, you'll see the message "Your request has been sent to the server. Waiting for response...". Once the process has completed, a "Download Results" button will appear. Clicking on this button will pop-up a new "Select location for download" dialog box, which will allow you to select where you'd like to save the resulting zipped j5 output file.
For more information on what is contained within the zipped j5 design output file, refer to the "Distribution of PCR reactions" page and the "j5 output -> Downstream automation" section in the j5 user's manual.