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This changed when I switched from the old mail system (POP) to the IMAP system. These are not Mac programs, but email systems ("protocols") that the server (e.g. your university email system) provides. Today, most servers let you choose, and most, nay every email program will support both; Apple Mail, Eudora (old and new) and others. Webmail is by definition imap, and so are Google Mail and MobileMe. (Check with your university system what options you must set for imap with their setup.)
If you read email on two or more Macs (or PCs, or in a web browser), imap makes things much easier. The point is that all your mail is stored on the server and each Mac accesses the mail stored there. I held off because I thought this meant I could not read old mail when I was offline. But no, a copy of everything is also transferred to each Mac, so you always have access to it, on- or offline. That sounds like "leave on server", the mail is both on the server and on each Mac. But the difference is that the mail you sent, as well as unifinished drafts, is also stored there. And, in particular, your email folder structure is also stored on the server. So once I sort a read email to its mailbox, it will be there whether I read it on the Mac, iPhone or on the web (iPhone Mail has some way to go before multiple mailboxes are really convenient, but anyway).
Imap is for all computer types. What about specific issues for the Mac and (Apple) Mail? Each mail server may have its own issues with imap setup. Mine refuses to let me create folders within folders. Instead, I must create the folder with a subfolder inside in the "On my Mac" section [which is the mail stored locally on your Mac only, you can have such as well], and copy them over to the imap section. I am also not able to sync "To Do" tasks between Macs. Such are neat in that you can point directly to a word in an email, assign completion dates etc., and they sync with iCal. But my iCals sync through MobileMe, while the mail syncs with imap on the campus server. And they do not work together. I may get a task to the second Mac, but then the link to the email is lost (I have discussed this elsewhere).
Mail also has "smart mailboxes", and methods for automatically sorting incoming mail (filters, in Mail called "rules") to specific mailboxes, these are part of the Mail program, not the server's imap system. If you have a MobileMe account (below), you can sync these settings between Macs, so you only need edit a filter once, and it will be used on every Mac. Sadly, that part of MobileMe sync will disappear with that service next summer, iCloud will not sync these mail settings, so you will be back to remembering what criteria you actually set up and repeat them on each Mac.
Address book, Calendar
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Anyway, this requires MobileMe which is going away to become iCloud (opened last month). This system only works with Lion, and as I will try to avoid Lion as long as I can, at least while MobileMe lasts (next June), I wondered if I also had to keep off upgrading my iPhone to iOS 5, as that uses iCloud. Apple does not say if you can still use MobileMe with iOS 5, but after searching on the web, user experiences seem to be that you can. I have not done it yet, but it appears thus I can upgrade the iPhone to iOS 5, and still have it sync with my Snow Leopards using MobileMe. Until next summer.
Files: iDisk and DropBox
So much for the small and automatic stuff, the next Big Thing is the documents we are working on. Perhaps you do different things at home than at the office, but like most academics I take stuff home to work on in the weekends or evenings. From floppy disks, I graduated to saving a copy of relevant documents to some online server and then copying back from there to the other Mac. For this, I could use my campus server, but once I had MobileMe, I could access Apple's iDisk as the go-between. It wasn't very fast, and of course you had to remember to copy back and forth and accrued many versions of the files that could be confusing. Another MobileMe feature, which I rather like, is Back to my Mac, which allows me to access my office Mac directly from my home Mac (and vice versa): I can see it as a volume in Finder and copy directly back and forth (so I am certain I get the latest version), or even see the actual desktop and operate the remote Mac as if I am in front of it. Very canny, but it works only under certain network conditions, and not if the remote Mac is sleeping.
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The only thing to remember is to save (and preferably close) the document before you leave the first Mac; if both machines have unsaved changes to the same doc, DropBox will (so they say, have not tried) notice this and save each as a separate copy, so you have to figure out which is which. But it should be second nature anyway to save the file you work on when you leave the Mac.
DropBox also works as an extra backup, because you then have separate copies on each Mac as well as on their server in case one Mac falls into the sea, and they there also keep older versions a bit like a surrogate TimeMachine. Or even better: A colleague of mine soaked her iBook with water the other day. Clean water, so she just left it to dry out and it worked fine (well, the screen sloshed a bit). But she needed her files on that particular day while it was drying. She had a backup with TimeMachine on a TimeCapsule, but what good was that? We realized that TimeMachine is fairly restrictive. It will restore old files to the original Mac only, or to a direct clone such as a fresh hard disk. In our case, we wanted to access her files from another Mac, using her account name and password, but the TimeCapsule would not hear of it. When we tried to connect to the capsule from another Mac with her identical account settings, it saw just the hardware Mac, not the account, as a new client (which is logical, since Time Machine of course also backs up system settings, not just account data, and the system was different). Maybe if we had TimeMachine on a physically connected hard drive rather than the wifi Time Capsule, we could have accessed the volume directly, but that was not an option. Here DropBox would have been a better solution, had her files had been on that server, she could have just picked it up from a web browser.
That is because you can also access your DropBox folder on the web, so you can get to your files there in a browser on any Mac or PC and copy to that machine, as well as to your iGadget. There is a DropBox app on the iPhone, in it you can read but not edit the file, and only the basic document types are supported for reading, thus not e.g. FileMaker databases. But it can "send" the DropBox file to other apps that allow you to open and edit; thus my databases (now all on DropBox, remember) can be downloaded and passed on to the FileMaker Go app (the "official" Filemaker for iPhone), which opens it normally. Of course, that is then a separate copy and changes made to the file are not reflected back to DropBox; I would have to transfer the file back to a Mac via iTunes, but still, being able to access to all my databases anywhere is great, even if just for reference (have I actually bought this book I see in the bookstore? Ah yes, I did.)
For example, I have an app ShowAnytime which allows me to display PowerPoints directly on a VGA screen from the iPhone, without using a PC or Mac. It can pick up files from my DropBox folder, so if I am on the road and something happens to the provided PC (which it often does), I can instead just connect my iPhone to the video cannon, download the file I left at the office (in the DropBox folder). Without having to plan it in advance, just as long as I have the iPhone-to-VGA cable with me in my backpack (it never leaves).
I said DropBox is free, that gives you 2 gigabytes storage, you can get more with a subscription, but 2GB for current projects and all my Filemaker stuff is enough for me. There are other similar solutions, but I am quite happy with Dropbox.
Notes and stuff: Evernote
Those are the big things. But then there are piles and piles of stuff that also syncs, as I said, I am not sure I remember all accounts I have any more. The blog you are reading is edited in Blogspot, which syncs my draft to my account with them, so I can write on it anywhere (that is why they get so long). Blogspot is part of the Google empire, which is also heavy on syncing if you have a Gmail account (gives you access to everything). If you do not need very advanced word processing, you can write your files in GoogleDocs, from anywhere.
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I have also discussed the "ToDo-list" issue, where syncing was an issue. I have for the moment stayed with WunderList that I mentioned there, but maybe look into the Omni alternative suggested by a comment, when I get back to that.
Specifically for academic purposes, I have also elsewhere discussed citation and bibliography software, that is alternatives to EndNote, and suggested the program Sente, which is what I mostly use. This also syncs my bibliographic database to its server, so that when I add a title at home, I have also access to it at the office. Several other alternatives also do this. It has worked fine so far.
Evernote
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However, I came up with one particular very limited purpose, and since it is also free, I have started using it for just that: Storing web pages. There are of course many specified services for this, like Instapaper and others (and in the latest version of Safari, more of which in a moment), but the idea for me was not to find a way to delay reading web pages - they pile up, and if I can't read a page now, I will never get the time.
But, at infrequent intervals I come across references to books I might like to buy at Amazon (or elsewhere). I can't buy everything the moment I see them, so the ideas must be stored to be prioritized later (and not in Amazon's wish list, please). I actually began creating Safari bookmarks for each Amazon page, but that was cumbersome. Perhaps Evernote could do this for me.
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Because, this "web clipper" was excellent in Safari up and until the latest Safari upgrade a few weeks back. Then it broke down; Safari has done something so the elephant icon no longer works. Happily, I read a warning about this before being asked to upgrade from Safari 5.0 (OK) to 5.1 (not OK). If you have already dutifully done what Apple told you and installed a full system upgrade in the last month or two, then unfortunately, the train has passed (you can upgrade the other elements, just deselect Safari). A few days ago, Evernote released a new "extension" for Safari that should supposedly restore the web clipping function, but that did not work at all for me with Safari 5.1 under OS 10.6.8. Maybe it is made only for Lion. Anyway, it wasn't quite the same thing. The original extension copies the web page directly to Evernote on your Mac (from where it is synced later to the server). The new cannot do that, it instead copies the page to the server, and it is later synced back to your Evernote collection. In any case, it didn't do anything of the sort, it simply refused to load or do anything.
There is another "recommended" option, which is to set up an Evernote bookmark in Safari. That does work in Safari 5.1, and again copies the web page to your account on the Evernote server. But while the original web clipper gave you a perfect copy of the page, the bookmark does not. Most of the html disappears; you may get the text (with some code around it), but not all images etc. So, if you want Evernote to clip web pages, hold back on upgrading Safari beyond 5.0. (I was able to downgrade by dragging a copy of Safari 5.0 from another Mac back to the one I had upgraded. No, Time Machine did not work here either, it reinstalled something that was not an application, just a folder.)
Will it iCloud over?
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What other syncing software do I have? iSync of course, but for my purpose, it was only used for linking mobile phones, it is not relevant for my iPhone, but I used it for my old Nokia. Then there is the paraphernalia of social networking things that evidently sync, they are often actually web services, not Mac programs, but several of them have corresponding Mac programs that do pretty much the same thing as the web site, such as Skype, Spotify, Wimp, Twitter (for me: Twitterific) and others have indpendent apps for Mac as well as iPhone. For all these, and for Facebook etc., you can of course just as easily use your regular browser.
Keeping track of the account names and passwords for all these services are another matter. Some log you on automatically, or keep you logged in for long periods of time, so you should be aware of who can access your computer(s). For others, you must find your own system of how to remember it all. But in any case, while you should perhaps not keep your head in the cloud, you can keep pretty much everything on your Mac in some cloud or other by now. Even without the iCloud.