How I sync, backup and use the “cloud” between my computers (and mobile devices)

I use at least 2 computers on my daily basis: a MacBookPro laptop and a MacPro desktop computer (plus two iOS devices: an iPhone and an iPad). For quite a while, I always struggled with those times when I was at one of the computers and needed some file or data that was actually stored on the other.

There are at least some sort of info and data that I really want to be automatically synced in all  my devices, so I ‘ll try to list below the different solutions I’ve found for each case (suggestions for others options are most welcome). As a disclaimer, most of my devices are from Apple (computers, mobile devices, etc), so I mainly live on an OSX/iOS world – nevertheless, I think some of this tips are also valid for any other platform.

1. Email: I have a bunch of email accounts (work accounts, gmails accounts, iCloud email accounts, etc). For all of them I use IMAP as a way to sync all my email messages (received, deleted, moved, read, flagged, etc) in all my computers (I use Apple Mail as my preferred email Client on all my computers). Works quite nice, and I always have my email “status” synced over all my devices (including the web, for things like GMail or iCloud mail). The only drawback IMAP may be dependent on the size of your email account (in GBytes) – IMAP works by keeping all your email in the server, so you need to make sure your email provider has enough space for your mail history (otherwise, you’ll need a “backup” strategy, which I find quite annoying…). For my work email (where mail inbox quota is quite small) I redirect all the emails to a specially created GMail account, where I have sufficient server space for all my email since 2005).
2. Contacts/Address Book: because I’m on OSX/iOS, I use iCloud to sync all my contacts (or address book) between all my devices. iCloud also allows to access your contacts form any web browser in any computer, which is nice in case you are nowhere near any of your gadgets and need to fetch a phone number, address or email contact). I know you can also try to sync your Contacts using Google/Gmail, but because I get iCloud for free on the Mac, I just use that.
3. Calendar: similar to the contacts above. iCloud syncs all my appointments and contacts over the cloud, also allowing me to access my calendar using a web browser. Once again, Google also provides similar funcionatilities.
4. Notes, clipping, papers,etc: for notes, web clippings, etc I just use Evernote, which has a “cloud” repository of all your data, that it then syncronizes using the OSX and iOS client in each device. For Research papers I use Mendeley, which also stores a cloud repository, that you can then use to sync in all your devices using the native app.
5. Documents, files and folders: for syncing a selection of my files between my computers (usually, all the ones on my OSX account “Documents” folder – I don’t feel the need to sync Apps or any other stuff), I use DropBox. I have more than 15 Gbytes on my Documents folder (and growing), which I wanted to be automatically sync’ed between my laptop and my desktop Macs , without the need to have them both powered on and somehowto access files that I would have spread over both of them, or to manually sync them using some  script using rsync or similar terminal stuff. So having them both automatically sync’ed in realtime to the cloud (using a somewhat expensive DropBox Pro 50 account, though) fixes this issue (and at the same time backing up files to the cloud). Now, Dropbox only syncs one special folder in your machine (as soon as you install it in your system, that is – the “dropbox” folder in your home directory in OSX), and I wanted to keep my documents on my OSX native “Documents” folder. There is a solution (which is the one I use and works quite well after the somewhat involved initial setup) that allows you to somewhat circumvent this limitation using UNIX symlinks (or a nice utility known as MacDropAny), and you can check how to do it here and here. Though, lately there is number of interesting (and cheaper?) alternatives to DropBox, such as SugarSync, that already allow you to choose any folder in your system to sync to the cloud (you can check a quite comprehensive comparison between the most well known cloud services available today here).
6. Application settings/data: Some apps (e.g. Omnifocus, 1Password, etc.) offer you the ability to sync their data among different machines using the cloud, and DropBox (given its well documented and widely accepted API) is one of the most well supported cloud services. I try use this feature whenever possible (and try to choose apps that support DropBox or some proprietary cloud syncing) so that when I open an app in my laptop I get the exactly the same data as when I opened it (and eventually added/deleted data into/form it) last time on my desktop computer (and vice versa). Annoyingly, one of the most frustrating situations where I still haven’t managed to have this “app sync” working is with Apple iPhoto (where I store all my photos) and, why not, Apple iTunes (there is that “home sharing” feature on both apps, but that requires both machines to be on and on the same network, which, as I’ve explained above, is not what I’m looking for).
7. Backups: not related to syncing, but probably even more important, is to have an actual backup strategy. Since I’m in a Apple ecosystem, I use Apple’s TimeMachine for all my computers to backup them into two HDs connected to a MacMini I have powered on at my place 24/7 (which also serves as my Media Center, being connected to my TV, and a Drobo “RAID” system where all my movies, tv shows and music live). It works quite well nowadays (long are gone the initial glitches and hiccups from OSX 10.5, when TimeMachine was first introduced). My laptop detects when I connect it to my home wireless network and automatically starts the TimeMachine backup without any intervention from my part (and so avoids me having to remember to backup frequently… which I wouldn’t). Because I’m a bit on the paranoid side in what regards backing up (I’ve lost my entire HD from a MacBookPro I used to have a week before my PhD defense – luckily I already had a TimeMachine backup at that time, which I could use to restore all my system back into an external drive in about 2 hours, and then use it to boot my brother’s MacBookPro – which didn’t even have the same specs as mine! – and do the presentation for my defense! ;-)), I also use CrashPlan for scheduled machine-to-machine backups (mostly between my MediaCenter MacMini and my MacPro desktop – I’m not using their cloud backups for now).

REFERENCES:

• Keep Multiple Macs in Sync with Dropbox
• Google Drive vs. Dropbox, SkyDrive, SugarSync, and others: a cloud sync storage face-off | The Verge.
• OSX: Bibliography managers

Public and private keys, digital (code) signing and Apple’s Gatekeeper

A peek behind the Gatekeeper | Agile Blog.

A nice and layman introduction to encryption as used for digital signing, based on private/public keys and Certification Authorities (CA), and how that relates to the upcoming Gatekeeper security feature of Mac OSX Mountain Lion (10.8).

Apple Serial Number Info // Decode your Mac’s serial number

Apple Serial Number Info // Decode your Mac’s serial number!.

How to get OS X to mount drives on boot rather than login and leave them mounted when you logout

TOLIS Group KB — How to get OS X to mount drives on boot rather than login and leave them mounted when you logout.

OSX: Tips & Tricks for Mac Mgmt

Tips & Tricks for Mac Mgmt, by JohnD.

Must read.

OSX: Setting permissions and ACLs

Nice article about how to setup Permissions and Access Control Lists (ACL – i.e. permissions on steroids ;-)) in OSX.

Another article from Ars Technica (although specifically about 10.4 Tiger, things should not be that different in 10.5 Leopard – it’s UNIX after all).

A basic tutorial on OSX Users, Groups and Permissions, and how to manage them.

And a some what related article about File Sharing in OSX can be found here.

OSX: Bibliography managers

Managing bibliographies, papers, the corresponding PDFs, matching metadata from Google Schoolar, IEEEXplore, CiteSeer, Web of Science, etc, can be a really frustrating (infuriating?) task.

I write most of my scientific papers in LaTeX (and I also did so for my PhD thesis), using the nice TexLive/MacTex distribution for OSX, which includes not only the Tex libraries and compilers, but also an editor (TexShop), a bibtex manager (BibDesk), a really nice equation editor (LaTeXit – this can even be used with MS Word or Apple Pages – see LaTeXit documentation), among other assorted and LaTeX related tools.

However, while managing bibtex files is quite simple (and made even simpler and snappier with BibDesk – I did it that way for my PhD), it still lacks a way to simultaneously find, match and manage the corresponding PDFs from the most well known reference services available (most of them requiring a paid subscription) in the internet (luckily all universities in Portugal have access to most of those services by means of the b-on initiative – that’s a good use of portuguese tax payers money! ;-)).

So, I’m looking for a swiss-knife solution for my bibliography needs, which can fulfil the following requirements, in order of importance:

1. Import/Export bibtex, so I can use it with LaTeX, and also provide an open and simple and standard bibliography format that does not get obsolete over time;
2. Provide a nice GUI for adding and managing references to the bibliographic database, where the metadata can be conveniently input and queried;
3. Have the ability to search for papers from the GUI, using the most well known reference databases available in the internet (IEEEXplore, CiteSeer, Google Schoolar, JSTOR, ACM, Web of Science, etc), and get the correct bibliographic metadata;
4. Have mechanisms to facilitate the retrieval of the PDFs corresponding to the papers in the database using the web services mentioned in the previous point);
5. Manage my papers PDFs in a iTunes like fashion, so that I can always find the PDFs in my harddisk, using the GUI as a query interface;
6. Provide some way to cite in MS Word 2008 and Apple Pages 09 (yes, some times, mainly when writing grant applications, project deliverables, and other boring paper work, I’m forced to use MS Word, or, if possible, Apple Pages);
7. Allow to perform annotations in the PDFs (although this can be easily done using an external application like the Preview app of OSX or Skim)

An interesting application I recently found that somehow fulfils some of this requirements is Papers. It allows to import my bibtex bibliography (although I’m getting some minor issues with this) and then easily look for the PDFs of each publication using Papers internet search services. It then automatically manages the bibliographic data (which can be exported back to several formats, including EndNote format, bibtex, among others) as well as the PDF files, in a very similar way to what iTunes does for your music collection.

There seem to exist other alternatives to Papers, like Sente, Bookends and the infamous EndNote, which although not being all the same and each package having unique abilities, they all provide a range of similar features in the end of the day.

I’ve actually installed trial versions of Papers, Sente and EndNote and I’m trying to see which one suits my needs the best.

Regarding Pages, there exists a quite simple way to export a selection (or the entire set) of papers from the database to MS Word 2008, which then uses the internal Word bibliography features to create citations and bibliographic lists, avoiding the need of any other software package (like EndNote). In case you find MS Word 08 citation styles limited (which they are – only 5 are provided!), there is a way to “install” additional styles of citation. With this, MS Word finally becomes somewhat usable for scientific works. 😉

Another nice feature of Papers (and Bibdesk) is that  when you export the bibliography in bibtex format, and open it in Bibdesk, the PDF files you attached in Papers (and keywords) show up in Bibdesk (check more info here).

Sente already provides a proprietary mechanism to work directly with MS Word 2008 (not sure about Apple Pages though), and EndNote provides a Cite-While-You-Type (CWYT) feature (for Word 2008 and Pages 09), which I think it’s only part of the package that justifies installing it (EndNote is really ackward and suffers from bad software design…).

Finally, there is a new contender in the game, which is Mendeley, which allows you to manage your publications online (something I really do not feel the need at this stage), and even has a desktop version (but that still lacks most of the requirements I listed above).

OSX: 6 GIT GUI Clients

Ok, so SVN still works quite well for me, but there has been such a fuss about GIT and other Distributed Version Control systems (Bazaar, Mercurial, …)  lately that I took some time to install and play with GIT. And Sourceforge already provides support for these!

GIT seems quite powerful, but presents some big changes in the way you think about version control. Anyway, I really liked the idea of having in my box the entire code repository of a project, offline commits and efficient and flexible branching/merging. But for some tasks, using the CMI is really a show-stopper (yes, I’m really a “graphical” guy ;-)).

So I’m looking for a nice GIT GUI. Here is a compilation.

OSX: 12 SVN GUI clients

http://theappleblog.com/2009/02/23/12-subversion-apps-for-os-x/

I’m currently using svnX, but its GUI is awkward.

I’ve tried Versions and Cornerstone, but for paid software packages, they lack some advanced features (e.g. branching and merging).

If there is a software package that I really miss from my MS Windows days is TortoiseSVN… and SCPlugin is not there yet. :-\

OSX: Environment variables in GUI programs

From the site pointed in the previous post in this blog, I finally understood how to setup env vars for GUI apps in OSX! This was driving me nuts, but things are starting to make sense again! 😉

There is also an official Apple tech article where this info is covered.

Environment variables in GUI programs

A GUI program will inherit the environment variables from the process that started it. So if you launch a GUI program from the command-line, it will inherit the environment variables of the shell where you launched it.
But if you launched the GUI program via Finder (by double-clicking) or the Dock (or some other mechanism in OS X’s GUI environment), it will inherit the environment variables of the “loginwindow” process. To set such environment variables, follow the procedure explained in this Apple TechNote.
You need to create a folder named “.MacOSX” in your home folder (note that since there is a dot at the beginning of the folder name, it won’t be visible to a simple ‘ls’ – you would need to use ‘ls -a’) and then create a file named “environment.plist” in the ~/.MacOSX folder. Put the definitions of the environment variables that you want defined for all GUI programs in that plist file using a format like the following example:

DYLD_LIBRARY_PATH  String   /Applications/MATLAB_R2007b/bin/maci:/Applications/MATLAB_R2007b/sys/os/maci:/usr/lib:/usr/local/lib

PATH   String  /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

(You can use the “Property List Editor” that comes with Apple’s developer tools or a 3rd-party plist editor – or just an ordinary text editor if you are careful to get the format correct. You can also install a Pref Pane for setting environment variables, known as RCEnvironment).