In order to compile caDNAno, you'll need Adobe Flash CS3 with the Adobe AIR extension installed: http://www.adobe.com/products/air/develop/flash/.

It is probably necessary to edit the "AIR - Application and Installer Settings" for cadnano.fla.

1. Use custom application descriptor file: cadnano.xml

2. Digital signature: you can either create a certificate or just prepare an unsigned intermediate file to sign later.

3. Make sure you have correct paths for Included files:
cadnano.swf
cadnano.xml
icons

(If the icons folder is not included, the caDNAno will load as a blank screen)