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)