Can I copy the PDFs I have on my Mac to the iPad ?
I want to download them from example from Google Scholar with the Mac (or iPad) and then read them on the iPad.
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Yes you can, drop them into iTunes or email them to an account you can check via the iPad. You can choose to either read it in the Maill app or read it in iBooks. Or just use Safari on the iPad to go to http://scholar.google.com/ and download the PDF to iBooks right there.
There are 3 main routes to get PDF to your iPad:
Which one is best depends on your workflow, but knowing all three may help you be more nimble.
Use Dropbox. You should already be using Dropbox, of course, because it's awesome. But it's also one of the easiest ways to get docs onto your device.
Drop it in your dropbox on your desktop, fire up the iPad Dropbox app, download the file, and choose which iPad app you want to open it in. Ta da!