Ruminating…

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)
- 1Password
- Dropbox
- 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)
- NovaMind
- 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:
Xcode
LaTex distribution
Unix software installation package (fink / app get)
GraphicConverter / MacGIMP
iLife

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!