The e-Office series now has a new home. All of the posts related to getting an efficient digital office workflow have been gather in single page. If you look at the menu-bar above you will find the dedicated button or you can simply click here
So far, posts in this digital office series this blog have tackled the hardware selection and components, OSX and iOS software, and finally the inputs or “Inboxes”. In this post, I will try to illustrate how all the pieces come together and making it all work.
Let’s briefly recall from part IV that for any document, either paper or digital, I follow the 2 minutes rule and the workflow diagram given below (click on it to obtain a high resolution image).
In my work workflow, I have a total 4 inboxes to deal with: 1) physical, 2) e-mail, 3) DevonThink Pro Office (DTPO) and 4) Things. However, the complete list of all projects and tasks resides in my electronic task manager, Things. Support documents are in DTPO and support e-mails in my Mail applications. The task manager has embedded links to get me back from a given project or task to DTPO or Mail. This is done automatically when a project or task is created from existing scripts (that comes with the task manager or DTPO, as will be discussed below).
Setting up a good structure is important. First you should do this for your task manager. The structure in my task manager follow closely that put forth in David Allen’s GTD book. I have:
- Areas of responsibility (20000 ft.)
- which can contains Projects (10000 ft.)
- and Tasks (here and now).
Things does not allowed for nested projects. So for very large projects, I will create an Area of responsibility with multiple projects in it. Otherwise my use of Things follow very closely this document by a Things user named goldencrisp87 and won’t repeat all of it here.
I have been saying that creating a good structure in your task manager is important because you will want to have a similar one in DTPO and maybe in your e-mail software depending how you organize your stuff. Example of Areas that I used (apart from the obvious GTD Next, Scheduled, Someday, Waiting For – I used a contact for Waiting For in Things since the very first OSX beta version):
Read / Review (manuscript, thesis, …)
Human resources (my students, one project each!)
University (teaching – one project per course and other faculty related projects)
Large research project 1
Large research project 2 (I have a few of these)
Infrastructures (lab and equipment)
Conferences-Travel (work related)
Delegated projects (I am not in charge of those but involved closely)
… and a few more Areas!
The relationship between the structure I am describing and the various applications I am using is depicted in the figure below (again click on it to obtain a high resolution image).
First at the top, my three main applications in term repository of documents, projects and tasks are given. Each project has is own project in Things and the associated mailbox and group (folder) in the other two applications. In practice, DTPO comes with a few AppleScripts that will make your jobs very easy. For example by selecting a document or a folder, you can generate an entry in Things with a link pointing back to that document or folder in DTPO. This means that any projects and tasks in Things which have support documents in DTPO can be connected. Similarly, if an e-mail is at the source of a task, the task can be created directly from Mail and the entry in Things will contains a link back to the e-mail (similar features can also be found in OmniFocus). Also, DTPO installs general “system scripts” which allow you to send mail attachments (documents!) or attachments and the associated message to DTPO. All those automated actions are described in the figure by the dashed-arrowed lines.
You will notice other applications in a second layer, which contains utility applications such as Address Book, iCal, Safari and Papers 2. Finally, the very last layer illustrates the mobile component of the workflow.
Digital workflow: Getting your inboxes to zero.
In dealing with my Inboxes, Things inbox is the last one I will get to zero. After my Calendar, it is the first application I will look at in the morning and the last before leaving work. My task manager is with me at all time having a sync copy on my iPhone and iPad (yes I did use Things Beta with cloud sync for quite a while, which has now been superseded with Things 2).
All attachments are transferred to DTPO inbox if important (to be classified later on). All e-mails are either discarded (trashed!), dealt with directly (2 minutes rule) or transformed into a task (created automatically in Things Inbox from Mail with a link back to that e-mail in the Things entry). On my employer IMAP server, I have four folders (you can click on the image below to have a better view of the structure in mail):
- Next Action for e-mails that are not part of projects, that I have to deal with and takes more than 2 minutes (entry in Things).
- OnGoing for e-mails related to ongoing projects in DTPO and Things. The substructure of this folder follow closely that of my task manager and DTPO. I could keep all of the e-mails of this category in DPTO with the other documents but I find it better to keep them on the IMAP server as it is accessible from multiple points (computer, web, iPhone, iPad, …). Furthermore, that e-mail system is maintained professionally and backup are handled directly by my employer.
- Finally I also use a Someday/Maybe and
- WaitingFor folders.
Notice that there is a no “Scheduled” folder. This is because either these e-mails will end up in my Tickler file system in DTPO or as a Calendar entry and move to the Next Action folder. If something contains a information or document to be used later on e.g. an invitation to event I generate an entry in my Calendar (this is done automatically in OSX by simple moving the mouse of the date/time in the Apple Mail app) and keep a copy of the invitation in my electronic Tickler file system in DTPO (more on that later on). Again a script transfer automatically the e-mail to DTPO Inbox as described above.
All important documents either for reference, for the Tickler file system or for a project are scanned on my Fujitsu ScanSnap 1500M, transfer directly in DTPO, OCR’ed and put in the Inbox. Physical documents are going directly to the recycling bin afterward.
Now that e-mails and paper entries are dealt with. We need to empty DPTO and task manager Inboxes. For DTPO one needs to decide if an entry is for future reference needed at a given date (Tickler file system), for a new project, belong to an existing projects or need to get assigned to a simple task (not really a project but should be dealt with).
I keep three main databases (I have a few more but for simplicity, I only mentioned those I used on a regular basis):
Note that my use of DTPO mimic that of regular filing cabinets to the extend of the structure explained in David Allen’s Getting Things Done.
The reference database is simple and uses a standard A-Z folder system (comes as a predefine option in DTPO). It is intended for documents (any kinds including clipping of websites!) that can be of used later on and as archive for completed projects.
The Daily database is the home of my electronic tickler file systems (e-Tickler), basically a digital version of the 43 folders technique (but with 366 sub-folders grouped in 12 folders, you get the picture ). The DTPO version of it is something I developed a few years back. The gurus at DevonTechnology made it even better. It comes with a script (which I have assign to a hot key – CMD-F14 in my case), which make an entry in iCal that something needs your attention on a specific date with a link to get you automatically to the specific DTPO folder containing your documents: based on the subfolder and folder you drop your documents in, the script will recognize the day and month and put a reminder entry either at that date in the current year or the next. Since your calendar should be the first thing to consult everyday, this is very efficient. I put all of my meeting documents there as well as any documents needing my attention at a specific date. Note that this e-Tickler works on 12 months cycle. Therefore, I also keep separate folders for future years as needed to temporary store documents I will need in more than 12 months. Once a year, I review these separate folder and redistribute the document at the appropriate place in the e-Tickler system. Finally, I further have a separate Read/Review folder where I put all of the documents I need review on short notice. The last important thing, I keep all of the folders from this database in the Sync area of DTPO as to sync on a regular basis with DevonThink To Go (DTTG) on my iPad (which is the tool I bring to meetings and do most of my reading/review from).
The OnGoing stuff database is just that. As per GTD, each project as it own folder. The overall structure will vary from user to user. In my case, the main category of projects follow the Area of responsibility in Cultured Code Things software as described in the previous section of this post. In Things, each DTPO folder becomes a project and a file can be attached to a task as needed. I used the Inbox in DTPO the same way as a physical IN basket. I throw everything in DTPO (using the Sorter) and when ready I proceed from top to bottom using the 2 minutes rule and using Things’ scripts described above as needed. This is another area where DTPO beats the competition for digital repository of documents: DTPO uses an artificial intelligence algorithm (AI) that help you sort documents in the appropriate folders / subfolders. With a good folder structure, the algorithm is right over 90% of the time, speeding up the classification process. Note that unique links assign by DTPO to your files (in Things for example) will not be broken as files are moved to subfolders!
I also keep all the elements from this database in the Sync area. When a project is fully completed, it is moved out of the OnGoing database and in the Reference database (and checked as completed in Things!). Note that you can throw about any kind of documents in DTPO including RSS and webpage. A nice tool is available for most browsers for clipping to DTPO directly. This makes it also a perfect software for about any kind of research projects.
A last note, DTPO can also index folders without importing its content. 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 this is only one way i.e. to DTPO not the other way around. I use this feature for my scientific manuscript PDF library which is managed by Papers 2 (this is described by a one way dashed-arrowed line from Papers 2 icon to DTPO Scientific manuscript folder in the provided e-office figure).
Making it really work
Here is an example of inboxes processing I am conducting:
Physical inbox: For every document, decide If it is not actionable and not important, it needs to go top the recycling bin. Otherwise scan the document and file it in DevonThink inbox. If it is actionable and less than two minutes DO it, if it would take MORE than 2 min. scan and put in DTPO inbox. At this time, it takes me no more than 15 min. per week ( I keep very little paper documents and now ask my colleagues to directly send me the digital files by e-mail).
E-mail: I get to inbox zero every few days or so, usually before leaving work as discussed previously. However, as I look at my e-mail a few times a day, I will for example generate on the fly tasks in Things Inbox if not urgent or deal with the e-mail directly if it takes less then 2 min. I will also move the e-mail in the appropiate folder (Next Action, OnGoing, … Or trash) directly. If the e-mail as a file attached to it, it will also go in DPTO inbox (using a script). So as the week move on, my inboxes both in DPTO and Things grows but everything that needed my attention within that time frame was already taken care of. What left in the inboxes are for the weekly review.
Next is getting DevonThink inbox to zero. Note that I must precise that for me the DTPO inbox is my main, large database Ongoing stuff Inbox not the global one. The reason for this is that DTPO AI for automatic classification of documents works with only one database at a time. If you put everything in the golbal inbox you would have to move them again before using the AI. Since most documents should go into either ongoing or new projects anyhow…Top to bottom following GTD process:
- Decides if its a new projects: if yes create a new group/folder in Devon followed by an entry in Things using the DTPO script.
- Decides if a new action is needed for each document. If yes, use DTPO script to generate an entry in Things.
- Use the AI to classify stuff in my database (or move manually if it is a new project).
- Move documents that goes into the Reference and Daily databases (Tickler file system – with entry by scriot into my Calendar and read/review as soon as possible).
- Repeat for all documents in the Inbox.
Things Inbox:I classify all entries top to bottom in the proper Area / Project folder. I will change an entry into a project if needed (all entry from the DTPO script are tasks by default but the change is a one click action Things and forces you to review what you are doing, which is a very good thing!)
- Review Project / Area and make sure next action is define (could be a Waiting For action) for all.
- Review tasks not attached to Projects / Areas
- Review Someday
- Review Schedule
Others: I will also once a week put all new PDF scientific manuscripts into Papers 2 and clean-up my DropBox folder.
By this point you should have a pretty good idea of all the commitments you have going forward i.e. what is on your plate. Simply review of next week calender items (your calender should be the first thing you open and close everyday anyhow) to be ready.
If you are new to this, program weekly recurring tasks in your task manager software (e.g. Things or OmniFocus) to remind you to perform all of these steps. Pick the order that make sense to you! Do set aside 2 hours weekly at first to do this. This will be well-invested time as it will saved you even more time in the future.
Two important tips:
1) The only way for such a system to really work is to use it and trust it.
- If you do not throw everything in, it will failed.
- Furthermore, if you do not review your projects / tasks at least once every week, it will also failed.
- Finally, be aware that developing a new habit takes 3 to 4 months i.e. for your brain to generate new pathways! This means that it will take you 3 to 4 months before you get use to this type e-GTD/e-Office approach. Before that time, you cannot really conclude if it is truly working or not.
2) Also important, is to figure out based on your level of activities what (and how much) software you really need. The goal is to get to an efficent and usable workflow while investing a minimum amount of time to maintain your set-up. if at any time you feel you are spending too much time “tweeking” the system and not enough time getting things done with it, it will be a sign that something must change.
In the previous posts, we went over the hardware requirements and selection, software and finally mobile software. It is now time to address the sources of digital documents, the true inputs of the digital workflow.
Not so long ago, there was a single inbox for all incoming “stuff” that requires your attention. Stuff is here define as anything that needs for you to decide what to do with it, including throwing in the garbage. In the analog world, that single inbox was the good old paper tray: correspondence, various documents, business cards, memos, telephone notes… everything ended-up there for further processing.
Nowadays, most of us have multiple mail accounts, each with an inbox(!). We get scientific manuscripts not by going to the library and making photocopies but rather downloading PDF documents from various services like arXiv, ScienceDirect and others. We received invitation to shared or get documents through cloud storage services (DropBox, Google, …). URL, RSS, blogs, etc… name your sources. Of course, we still get some old good paper documents. Let’s face it, it can be a mess.
You thought emptying that single physical inbox tray an impossible task, welcome to the digital era!
Let’s examine the various sources of documents in your digital life.
1. Paper documents. Yes it is still alive. I keep two physical inboxes, one at work and one at home. I will throw in it all paper documents, bills (at home), written notes (from phone call and others) and so on I received. I will usually empty it once a week. 99% of these documents will end up in the recycle bin after being scanned using my Fujitsu ScanSnap (scanned, OCR’ed and put automatically in DevonThink Pro Office inbox).
If you have not gone digital yet, this is were you are going to spend a lot of time at first, scanning those paper documents.
TIPs: If a document can be obtained in digital format, ask for it or download it instead of scanning from paper. At first you will need to remind your colleagues to e-mail them to you but after a while it becomes a given for everyone involved. Scan only your ongoing projects documents to start. This will leaving you the time to decide if you really need to scan your reference / archived paper documents.
2. On the fly information. This comes in mainly from a discussion in a corridor or one of these illumination moments. It is something you must remember and possibly take action. Two choices here. Write it down on paper and put it in your physical inbox or capture it digitally. I use either a task manager for this, namely Cultured Code Things (Mac/iOS only) or DevonThink To Go (DTTG). If you must work multi-platform, I suggest giving Wunderkit (free) a try.
3. Meeting notes: I use DevonThing To Go (DTTG) for all of my note taking. All notes get saved on the iPad and sync with DTPO on my Mac. It then make it to DTPO inbox for processing (again usually once or twice a week)
4. Web / Cloud sources: Any documents from these sources will go into one to two buckets: DTPO inbox or Papers (scientific manuscripts). Even clipping of web pages and RSS get be imported in DTPO making it an obvious containers for any and all project related materials.
5. E-mail: This is now my most common source of digital documents I received. It is quite likely that you are in the same situation as I am. With modern mail application (I use Apple Mail), you can have as many “Inbox” as you like. I usually collapse all of them to get a general overview of all my incoming e-mail. I easily receive 80 to 100 “good” e-mails per working day, less on weekend. E-mail are important but can also be disruptive from a getting work done perspective. This is one of the nice thing I rediscovered with the iPad, doing one thing at a time with your full attention, without being side track by all of these other applications requiring your attention all time.
TIPs: remove any incoming warning sounds or (Growl) notification. If fact, this should be applied to all incoming information (Facebook, twitter, …) as it is unproductive noise. Look at your e-mail only a few times a day (morning, before or after lunch, end if the day, …) and never look at your e-mail if you do not have the time or energy to deal with what your are going to find. Lastly, you should never have to deal with a given e-mail in your inbox multiple times.
In fact, whatever the type of inbox (physical, mail, …), you should never put something back in (or leave it in) your inbox once you look at it: you must decide as you look at it what do to, and yes this could very well be, “it will take time, I do not have time right now, will deal with it later.” If this is the case, a task should be generated in your task manager (with a reminder if needed or in your tickler file system if at a specific date). For an e-mail, once this task is performed, it should be moved to another folder entirely. Some might say, why not leave it in the Inbox… because an Inbox is just that: entering new information that have not been dealt with yet and it should always stay this way. Trust me, it works and here is how you do this (this is directly an application of David Allen GTD and it works miracle for e-mail):
A- For any input, if it can be deal with in less than two minutes, you should do it and either trash / recycle that input or keep for future use if needed.
B- If it cannot be deleted nor dealt with in two minutes you need to take a decision:
Ba- defer it to a later time
Bb- or delegate the action to someone else.
In either of the last two above situations, an entry in your task manager should be made. In all instances, nothing (and this includes e-mail) should ever go back in your Inbox (physical, electronic or e-mail). I usually get my e-mail Inbox to “zero” once a day. If you want to learn more about getting your e-mail inbox to zero, have a look at the Inbox Zero series by Merlin Mann.
I will tackle the set-up and workflow that I came to in the next post but I want to conclude this one with a sense of how the various software fits with the above decision process in relation to the various inboxes and source of documents. If you know the GTD book, the figure below will seems familiar. If not, I have taken this workflow from David Allen GTD book and I have superimposing on it the software (using their icons) described in part II and part III [copyrights notice: this composition is made solely for educational purposes. The workflow diagram below is from David Allen's book and the icons belong to their respective software creators].
The decision tree described before (A, B, Ba and Bb) can clearly be seen on this figure. Which application is attached to the various components of this workflow is also given. The full lines given the flow of decision. The dashed lines indicate automated actions (by scripts, system services and Automator elements) between applications. For example, the creation of a task or reminder for a document or an e-mail in Things is done automatically from DTPO or MAIL by script and system services. Even better they are assigned to hot-key combinations, which means all of this is generated in a few seconds for each entry. The other nice things is that a link is pasted automatically in Things note section of the task entry and if click send you back to the source of the task (directly in the originating application!).
In the included figure, you can switch Things for your favorite task manager. However, at this time on the Mac I do not think you will be able to reach this level of integration and ability to deal with a large number of projects with applications other than Things and OmniFocus. No, a simple task-only list application won’t cut as it does not scale.
Also, if you really want to stick with the Finder and folders/sub-folder structure for your documents (instead of using DevonThink), you might want to check an application called Things Folder that will help you keep a folder structure organize and in-sync with Things.
Part III: Mobile Software
10 years ago mobile software meant having a Palm is your pocket. At some point, I decided to change my Palm pilot for an iPod Touch. Combined with MobileMe, I had by address book, calendar, e-mail, browser bookmarks and keychains sync across all of my devices (home, office and mobile). Nowadays it might seems trivial with Google services and all…
In term of digital workflow, the iPad has been a revolutionary device for me. It replaces my paper tablets and papers documents in meetings. It is one of my most productive gears I have ever bought (productive here is synonymous of actually doing work with the device not spending time working on - as in tweaking – the device itself)
The applications I use often sits on the first screen, which is shown below. The key ones are in the bottom “dock”. The same major apps are also installed on my iPhone and work with the Mac counterparts:
- DevonThink To Go (DTTG): my files everywhere in sync with DTPO on my Mac. I also take all of my meeting notes in DTTG, which are then sync back to the Mac and are fully searchable moving forward. Without DTTG, you will still need another application that provide you with a “file system” for your iPad if you want to keep various kind of documents. Before DTTG became available, I was using Air Sharing. Nowadays DropBox app for iPad could play this role but you won’t get the benefit of DTPO-DTTG synergy. With DTTG, I keep a copy of all my ongoing projects and associated documents, my read/review folder and my electronic tickler file system (the electronic version of the 43 folders system). About 10 Gb of data give or take.
- iAnnotate : the best on the market I think. Handles PDF files and full annotation tool-sets. Results are compatible with acrobat and other PDF reader. In addition you can project any PDF document on a multimedia projector and annotate / write in real-time. It further accepts WORD and PPT that it transform on the fly to PDF (performance is not always on par with a print to PDF on OSX). The first application I bought when I got the original iPad and has been update consistently ever since. 10$ well spent! Note that the interaction between DTTG and iAnnotate is excellent. DT assigns a unique ID to each file. From DTTG you can get a file out for annotation and send them back again to DTTG. The unique ID will allow DTTG to replace the original file with the annotated one and later sync with your Mac database. Similarly, it is easy to get new files in DTTG from DropBox or Apple Mail. However, Pages, Keynote and Numbers do not play as nice in their current versions with DropBox and the like, and going through e-mail is the only option without going through your Mac (and iTunes).
- Things for iPad. This version is just gorgeous. I find doing my weekly review (GTD again) much more easier and fun on the iPad version then the Mac one. A fast and efficient cloud sync is mow in place (stable beta version). I almost never use the iPhone version now.
- Apple Mail: University Exchange server, iCloud, GMAIL.
- Apple Calendar: iCloud sync, Google calendar.
- Apple Contact: iCloud sync.
- 1Password for iPhone/iPad: It sync with its main database that sits in a DropBox folder (it is encrypted) when you have WIFI access.
- Dropbox: if you are worried of storing your data on a third party server, there is a nifty application (PC, MAC, iOS, Android, …) called BoxCryptor that offer support for DropBox encryption.
- Apple Safari: iCloud sync.
- Message / FaceTime / Skype.
- Reminder: For Family use as we share one reminder list, otherwise I use Things.
- Page / Keynote / Number.
- iTeleport: conecting to any Mac / PC from my iPad. Cool!
- Papers: companion to the Mac version.
- iThought HD: Doing mind mapping on an iPad is almost as good as on paper.
- PressReader: the digital version of our local newpaper subscription. No more dirty hand.
- Airport: I manage the Airport at home and at work with it!
- WordPress: this blog.
I am still search a good “scanning program” using the new iPad camera.
I also keep a bunch of other applications that I used more or less often, including a few games (like Civilization and tChess Pro). However the first 8 entries above I use everyday and, with their OSX big brothers, are an integral part of my digital workflow.
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)
- 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:
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.
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
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!