Digital Office II: Mac Software

For those who might not have read the first post in this series about the hardware side of things, please have a look: Digital Office I

Here is a list of the main software that I used regularly on the Mac as part of my digital workflow, including links to the most important one:

– OSX and its functionality (TimeMachine, AppleScript, Automators, terminal, …)
DevonThink Pro office (file database / working database)
Cultured Code Things (GTD task manager software)
– Apple iCal
– Apple Mail
– Apple AddressBook / Contact
– Safari (bookmarks sync to my iPad and iPhone via iCloud)
Papers 2 (my main manuscript database and citation software)

Cornerstone (access to versioning server)
– Microsoft office (not by choice)
– Page/Keynote/Numbers
Endnote X4 (for collaborative works I do not control)
MacUpdate (automatic update of software. I usually run this one a month as a repeating task in my task manager software)
– Acrobat Pro
– Skype / FaceTime

Other software installed and used once in a while:
LaTex distribution
Unix software installation package (fink / app get)
GraphicConverter / MacGIMP

The first 10 applications above are the cornerstone of my digital workflow. The main reason it works so well I think, for me at least, is because up to now it proves to be scalable to the level of ten of thousands of files as mentioned in my previous post . The second reason is that with MobileMe/DropBox and now with iCloud/Dropbox and the fact that all these applications have mobile versions (iPhone/iPad), I never have to worry about the simple stuff: passwords and digital wallet info are in 1Password, store in DropBox, accessible and in sync on all my devices. Same for contacts, bookmarks, calendars (including Google calenders) and tasks (Things beta brings a highly efficient could sync across all devices). Finally with iPad (and iPhone version) of DevonThink and Papers, it is relatively easy get your important documents with you and accessible at all time.

File database

Before DevonThink, I tried multiple ways to deal with all the files gathered when going digital. The basic approach is to set-up an efficient folder structure and hope that in combination with the system wide search engine it will be enough to find that important documents in a few seconds when needed.

The next step is to add tagging to you files. There are multiples ways of doing this. At the time, and after trying a few options, I had adopted Together for which you can use your optimal folder structure, add tags and a few more useful trick. Unfortunately, these software do not scale very well to a very large collection of files. This is the time to turn to a true solution: DevonThink

DevonThink is at the center of an efficient, scalable and robust digital workflow. DevonThink is probably the best file database application available on the Mac. In my opinion, it is the only viable option that meet the requirements set forth in my first post and still be scalable to the level needed if you are serious about going digital. First it handles a load of files (and file formats) easily. It performs full indexing of contents of files, an operation that is fast and efficient. Search for files either by name or based on the file content works in seconds even for large databases. Tagging is supported if you feel it is needed (in addition to full indexing – I really see the need to use it). DevonThink allows for advanced search using boolean operations and also across multiple databases.

There are various version of DevonThink, the one I use is the Pro Office (DTPO) which handles OCR from scanned PDF document (the Fujitsu scanner scans directly to DTPO), multiple databases and more. DTPO is highly scriptable and I use many of the scripts, including clipping in the web browser and mail action scripts, on a regular basis. It also contains many predefine data structures (you can create you own but that is for another post). I certainly will not give a full accounts of DTPO capabilities here. You will find the e-book by Joe Kissell is an excellent reference for beginner and intermediate users.

Note that my use of DTPO mimic that of regular filing cabinet to the extend of the structure explained in David Allen Getting Things Done. I keep three main databases (I have a few more but for simplicity, I only mentioned those I used on a regular basis): On Going, Daily (an electronic tickler file system – see picture above) and Reference. I will detail this usage more in a future post.

A last note, DTPO can also index folders without importing its contents. It will allow you to search as if it were imported by frequent synchronization either through the menu or attaching the sync script to the DTPO folder of interest. Note that is only one way i.e. folder to DTPO not the other way around. I use this feature for e-mails and my scientific manuscript PDF library which is managed by Papers.

Added Note (June 13th):  DT does not modify your files in anyway i.e. .doc remains .doc files. Furthermore, at anytime you can export your database back to regular Mac “folders”. So you are not lock-in.

Dealing with scientific manuscripts
I have used bibtex as a graduate student and postdoc but it lack the modern PDF handling needed nowadays. Zotero is an interesting alternative I used for almost a year. I discover Sente at the time. A superb interface, excellent PDF library, in-application search of PubMed, word processor citation handling and export to Endnote and bibtex. I used version 5 and 6. However, Papers 2 (starting at version 2.0.8) won me over with its highly efficient on the fly citation tool and I have used it ever since. So any PDF related to scientific publication, published proceedings or abstracts and so on does directly in Papers (and sync in DTPO as explained above)

Contact, calendar and mail

For contact, calendar and mail, everything can also be integrated with Google instead, but somehow having Apple hardware all around make using Apple software much more sense. As a bonus Apple applications tends be much more stable (plus I prefer Apple privacy policy to that of Google for now).

Task manager
If you are serious about task management, dealing with a few hundreds of them at any one time and maybe close to 100 active projects (with 30-40 pending/inactive ones) there is only really two choices: OmniFocus (from OmniGroup) or Things (from Cultured Code). Bottom line, CC Things has a much simpler interface and allows for increased flexibility in how the tasks (and review) are handled. Things unfortunately does not have the notion of parallel and serial tasks and that of nested projects but this is relatively minor. With the ongoing public beta, Things now have an efficient and fast cloud sync solution which I am now using as my daily “production” option.

Passwords managements (and “digital wallet” information repository)

Finally 1Password is one of those utility application that change the way you surfed the web. It manages your password for any sites and can filled forms with various information without typing (read bypassing possible keylogging). So you can have only 1 strong password to remember but use safely different and unique strong passwords for many sites / accounts you have on the web without never “forgetting” any!

Posted on June 11, 2012, in Internet Ressources, Research and Academia, Software, Technology and tagged , , , , , , , , , , , , , , , . Bookmark the permalink. 26 Comments.

  1. Hi Luc, when speaking about task managers, did you try 2Do for Mac OSX ? One advantage is that it syncs with iCloud and, therefore, with Apple’s Reminders. 2Do Iphone and iPad are excellent too. I was a former Things user and am now testing 2Do.

  2. Hi Luc, if you don’t mind yet another question/comment for your June post… I have a lot of info in DTPO organized by topic (in groups) and pdf articles in Papers2 by topic (in collections). It looks like there’s no way to ask Papers2 to create collections in subfolders so that they will (via DT indexing) show up within each corresponding DTPO group. Therefore I’m considering importing all of my pdf files into DTPO and using Things2 just for citations. (Not great – but otherwise I end up with a huge single folder of pdf articles in DTPO.) Any other suggestions? Given the number of people who seem to be using both Papers2 and DT, I’m surprised there isn’t a way to do this!

    • The indexing function in DTPO work from your Papers2 collection folder (and sub-folders). So basically, any organization you are using for your PDF with Papers2 will be replicated in DTPO. I am guessing that what you are alluding to is that your Papers2 and DTPO folder/subfolders arrangements are different?

      I must say, I do not bother so much about folders and sub-folders structure for my scientific manuscript collection (now close to 4000 entries), since I am using the search function to find what I need (the indexing is quite powerful and you can combined information using Boolean operations for advanced search).

      • hi Luc, it sounds like I’m missing something – I haven’t found a way to import my Papers2 articles into DTPO and preserve the collection structure. I would like to have the same arrangement in both, but in Papers2 I get either one folder of files or a set of folders based on author/year/editor (options in Papers2 preferences).
        I hear you, though, about the search function. My collection is still relatively small…

  3. Luc, thanks for this informative blog entry.

    Regarding the choice of Papers, did you also consider Mendeley? If so, I’d be interested in your opinion regarding Mendeley vs. Papers. I still sometimes work on a Linux machine so the cross-platform aspect of Mendeley was at first appealing. But now I am moving more completely to Mac (though still keeping a Linux box with a GPU for computations), so I am reconsidering Papers.

  4. Dear Luc, I agree with your workflow, very similar to mine. Only one big difference: in my opinion Bookends by Sonnysoftware is by far superior to Paper 2.0, in particular when you are dealing with 30.000 PDF or so (I’m working in classical studies, so the amount of [electronic] paper is huge!). I will follow your posts with deepest interest.


    • Wow an accumulated literature of 30 000 PDF is impressive. I must say, I have no idea how Papers would behave is this situation (I have only about 3600 PDF). I will certainly look at Bookend in the next few weeks.

      One of the thing I really like about Papers is the way you can call-up your library and insertion citation while you write. Similarly to utility applications such as QuickSilver or Alfred, touching twice the CRTL key at any moment brings-up a small window where you can search your library (without even having Papers running!). If in a word-processing application you can simply insert one or more citations and format when ready. Very clean, simple and streamline workflow.

      • With bookends the possibility of different citation paradigm is completely customizable. You have more filters for importing references from on-line databases than using Papers. Papers has a better looking but Bookends is more robust, and with an iPad companion (Bookends On Tap) such as Papers. I am puzzling with your very interesting organization with DTPO. It would be nice to have the Apple Script automating all the features you have so beautifully explained. I am a Things user like you. For writing I prefer Nisus Writer Pro and, for serious projects as books, Scrivener.

        • I am puzzling with your very interesting organization with DTPO. It would be nice to have the Apple Script automating all the features you have so beautifully explained

          Which portion is part of the puzzle?

  5. I tried DevonThink for about a year and I think it’s actually quite a crap. At least for the document management it has almost no functionality and a really bad user interface. Among all typical things you want to do with the scanned pdfs it fails in every manner: there is no simple way to edit creation date of the document to sort chronologically (you need to call an “alert window” with a special script for that which is deep in folders), editing author of the doc requires calling out floating overlay from another menu (to be able to sort by sources), scanning interface is a nightmare, OCR function bloats file size from 200kb to 3Mb (though my ABBYY Fine Reader Express makes almost no changes to size at all), lots of functions (like import from Evernote) simply do not work. There is no sync, no reliable back up, I don’t mention such things as lists of dynamic suggestions to reduce the mistake probability by typing over and over again same names. I know there is no much similar products at the moment on the market, but that doesn’t make a good app out of this ****.

    • Well your set-up look rather non-optimal. I have been using DTPO for many years now and I have scan thousands of pages with my Fujitsu scanner. I found the interface not only simple by highly efficient and drop the document directly in DPTO for OCR (or to CardIris for business card scans). I found the OCR bundled with DTPO software excellent (never had to re-scan a document yet) both in French and English. The AI for document classification is also performing quite well. I am not an Evernote user so I cannot speak from experience but you should clearly look on the Devon forum because many DT users are also Evernote users.

      Sync: not quite sure what you are looking for. There is no official Mac to Mac sync yet (but there is a beta plug-in available if you want to try). Sync from Mac to iPad/iPhone does work nicely for me. For back-up, I simply use time-machine to a raid device for the past 2 years, no issue there.

      I am not sure what you are searching for in document management. DevonThink is not SharePoint or any other open source versioning-like system for files that is for sure. I am not also convince that you could easily change creation date and other important feature on a true, professional document management system (especially, if you want to keep legal value, but again I am not an expert here).

  6. Luc, thank you for such a great series of articles!

    I have pretty much the same setup as you do. I am just wondering how I can combine the various apps better – I thought of scripts, but writing them became very difficult very quickly.

    So what would you recommend to push/automate information between Mail, DTPO and (in my case) OmniFocus?

    Is the DTPO Mail-plugin really the be-all end-all solution?

    • It actually depends quite a lot of your workflow.As I explain in my post, I do not systematically transfer my e-mails to DTPO. I do indexing however.

      What I do instead is to have project folders on my corporate (University) exchange server that are mirrored in DTPO and Things (OmniFocus) for you. When I do create a folder in Mail, I execute a script that make the necessary entry in DPTO and Things.

      Here is the script I used:

      — Import a selected MailBox as a GROUP to DEVONthink Pro and create appropriate task in Things.
      — Created by Luc Beaulieu, June 8 2012

      property pTags : “DEVONthink”

      tell application “Mail”
      set selectedMailboxes to selected mailboxes of front message viewer
      if (the count of selectedMailboxes) > 0 then
      tell application id “com.devon-technologies.thinkpro2”
      set myDB to open database “~/Documents/Devon/OnGoingStuff”
      tell database myDB
      repeat with theMailbox in selectedMailboxes
      set theMailboxName to name of theMailbox
      set theGroup to create location theMailboxName in myDB
      set theURL to (“[url=x-devonthink-item://” & uuid of theGroup & “]” & name of theMailbox & “[/url]”) as string

      tell application “Things”
      make new to do with properties {name:theMailboxName, notes:theURL, tag names:pTags}
      end tell
      — display dialog theURL
      — if not (exists current database) then error “No database is open.”
      — set activated to true
      end repeat
      end tell
      end tell
      error “One or more mailboxes must be selected.”
      end if
      on error error_message number error_number
      if error_number is not -128 then display alert “Mail” message error_message as warning
      end try
      end tell

  7. One thing to note is that DT is able to search in Office documents. EN cannot do that. That makes, for me at least, a very big difference !

  8. This is a great article, thank you. I am considering switching from Evernote to DevonThink. What do you see as the benefit of DT over EN? If I am on someone else’s computer and need my data, what options do I have? Thanks.

    • I my mind EN has a different purpose than DT and can be used in synergy. I would agree that if you have very little digital documents, EN alone might be ok but not with thousands: it is not a scalable solution.

      DT is a true digital document management systems, while EN is great to take notes on the go, including capturing a picture or a webpage. I would say any ideas for which you have not yet taken action or move to an actual project could stay in EN. Once this step is done, any information in EN should be transferred to a DT folder (group) for further actions.

      • Thank you for the reply and this series, it has been most helpful. I think I will give DT a little more thought once they get the dropbox sync ironed out a bit. I really need my documents on my iPad reliably as well as on all three of my macs.

        I have been using EN for a few years now and I am only at ~2000 notes not sure where the tipping point is but I haven’t reached, I don’t feel, so hopefully I wont before DT has the syncing issues fixed.

  9. fantastic . Thanks for informations . Ill be back. Thanks once more 66110

  10. I actually like your writing style, excellent information , thankyou for putting up : D. 259842

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