ALIS is the logistics system for the program that has an off-jet and on-jet component. ALIS takes the role of a traditional computerized maintenance management system and expands it to include an on-aircraft prognostics and health monitoring component. The idea is to have the jet tell you what's wrong with itself.
The article you linked to is about the F-35's mission systems software, which is really a software suite that encompasses all the computers on the aircraft itself. The MS software load provides all the stuff necessary to make the jet's hardware do what it needs to do to fight.