Integration with the JBEI Registry/Vector Editor/DeviceEditor and Clotho BioCAD platforms
The best way to use j5 is in conjunction with the JBEI Registry platform (including VectorEditor) and the DeviceEditor visual design canvas.

It is currently possible to copy/paste a highlighted sequence selection from VectorEditor onto a part icon in DeviceEditor, and this action will bring along with it any asscoiated sequence feature annotation information, and the sequence context of the selected sequence fragment (which is useful for identifying PCR mispriming events, as described in the Brief survey of j5 functionality).

A user's manual for DeviceEditor (along with demonstration videos) is now available. In brief, DeviceEditor serves as a graphical front-end for generating the input files required for j5 to design an assembly. With the implementation of the j5 XML-RPC web service, it now possible to run j5 directly from DeviceEditor, without the user having to separately visit the j5 simplified web page interface to run the actual assembly.

Now that the j5 XML-RPC web service is in place, it is possible to write a j5-plugin for the Clotho BioCAD platform (Xia 2011) (no immediate plans for this are in place, but it may be accomplished through a collaboration with Chris Anderson's group at UC Berkeley). In addition, with the XML-RPC web service documentation, it should be possible for anyone to write their own j5 XML-RPC client.

Following assembly design with j5, the goal is to enable the user to deposit the resulting DNA constructs "in progress" to the JBEI Registry platform. This feature is also under development. After running a design on the j5 server from within DeviceEditor, the user can now click on hyperlinks provided for each of the resulting j5-designed sequences. These hyperlinks will open the corresponding sequences in VectorEditor, allowing the user to immediately visually assess if the desired sequences were designed as envisioned.

Through DeviceEditor, j5 is thus connected to the JBEI Registry.