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NetLogo OS X 10.8 (Mountain Lion) Compatibility Info
If you already have NetLogo installed, you should find that it works fine on Mountain Lion.
Versions of NetLogo prior to 5.0.4 were blocked by Mountain Lion's "Gatekeeper" feature.
If you try to install older NetLogo versions on Mountain Lion, when you try to open the disk image you'll get a rather alarming-seeming dialog that says NetLogo is "damaged and can't be opened. You should move it to the trash." The OS is wrong; the application is fine. In order to open the disk image, you just need to open System Preferences, go to the Security & Privacy panel, and change the "Allow applications downloaded from:" setting to "Anywhere". For more details, see this Apple support document.
NetLogo 5.0.4 will still be blocked if your Gatekeeper is set to "Mac Store App" only, but instead of Gatekeeper telling you that the file is damaged, it will tell you that it was not downloaded from the app store. Setting your Gatekeeper to "Mac App Store and identified developers" will allow installation of NetLogo 5.0.4.