Reference System to complement OF

Hi all,

I am wondering what everyone’s reference system is. For every project I have (and for some things that aren’t projects) I want notes. Right now, notes are strewn across various programs, and I never feel like I know where to find or put new notes on a project or area of responsibility. I’m wondering if anyone has an ideal setup on this?

I know there is a notes field for projects already in OF, but the field seems very minimal by design. Also, I feel like projects go away when I complete them, so it feels wrong to put lasting information into them. Also, some areas I wouldn’t call ‘projects’ need notes too.

I don’t want anything that involves regular maintenance because I think that system will eventually fall apart for me. I just need a system where I can quickly add info to a topic, that is ideally linked to OF projects in some way so that I am not spending an hour a day just making sure they match up.

Is this remotely possible? I’d appreciate input!


I think it’s going to depend on whether the notes are only valuable for a project, or are emergent from a project but useful elsewhere.

I have a folder in the filesystem roughly corresponding to every project. Project-related notes go in there, as markdown and/or taskpaper files. If they’re linked to a specific task, I’ll create an OF note with a file:/// link.

I also have a bibliographic database (in BibDesk) and scripts that let me create a new OmniFocus task linked to a BibDesk item, and a linked file of reading notes on an item. My reading notes on journal articles for a project don’t go in the project folder, they go in a file linked to the BibDesk database, because even though they may be important for a particular project, in the longer term I want to be able to refer back to them without remembering what project it was that led me to first read an article.

Likewise teaching. Every course gets a folder (and an OmniFocus project). Notes specifically related to running the course go in that folder. Notes related to course readings, in contrast, go to the reading notes linked to BibDesk, because they will have value after the course.

Obviously your needs will vary but it might be useful to conceptually separate project notes from reference notes.

See also: . I’d been doing more or less what he describes for years previously, but he does a great job of articulating it clearly.

Once the conceptual work is done, there are loads of software options from nvalt to devonthink and everything in between (and simpler options like the Finder and a good text editor), but from what you describe I think figuring out the roles of different kinds of notes will be more imprtant than picking a particular implementation.

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Check out Curio It creates multi-meda scrapbooks for projects. Everything from images and videos to weblinks, mind maps and more. It’s an incredible app, and they are constantly developing improvements.

I build a Curio project for every major project I have to work on. All the notes, links, data and collateral research stays in one place. You can also embed any Mac document into the Curio project, so all your files stay in one place as well.

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multiple archives,
no proprietary format (ala Evernote)
transparent file structure
Secure, archives (if needed)
cloud sync, archives can sit on any cloud sync service
Excellent search.
Handles any file type.

I have an “in progress archive” for obviously WIP, a reference archive for long term article or web clipping storage, and a archive for code snippets. I also archive all mail into a separate secure bundle.

I also use nvALT for simple markdown code storage and for quick notes as I can access it via the command line and some scripts, as well as my code editor.

I’m adding regular actions with a dedicated context “Reference” into a relevant project. Most of the time I mark them complete when I’m done with the whole project; less frequently when an item is not useful any more (i.e. I’m done with this piece of project).

I also have dedicated reference-only “projects” where I store everything I need across projects.

In some cases, when I complete a project and there are some reusable items in that will be very likely needed in future projects (i.e. lessons learned from one vacation trip can be useful for future vacations), I move them to dedicated “projects” like “reusable reference from project X”.

I wish Omni have much more support for scenarios like the above; let me know if you (or Omni) need more details in how this setup works for me–and what’s missing.

I keep this material as notes in Evernote. Notes can hold all kinds of items - PDFs, Word Documents, audio files, jpgs. Evernote is available on all my devices, and on any computer via the web. It has an easy tagging system, so no matter what folder I’ve filed the item in, I can tag it for one or more projects. Each note has a link that can be copied and pasted into the notes section of an Omnifocus item, forming a clickable link directly to the note.

You could do much the same using OS X’s Finder if you use tags in Finder.

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EagleFiler also has tags, stores almost anything and unlike Evernote does not wrap an HTML layer round every note, or insist on RTF.

You can store on cloud services and access files through GoodReader on iOS. Unlike EN it does not have a subscription model or heaps of “stuff” bolted on for the sake of it, plus it’s available offline unlike a basic EN setup.

If you have not guessed I do not like the way EN has gone in recent years, and I would not trust it for the future, much less invest my life in it. I store nearly everything in PDF or markdown which pretty much future proofs it whatever platform.

Out of curiosity, what advantages does eagle filer offer over the file system?

OK a good question…

For me, I use it to archive and search for mail its search is lightening fast and the choice of what you display in record lists is comprehensive (tags date, sender etc etc.)

Libraries can be encrypted and password protected, this allows me to store sensitive stuff on the cloud for redundancy while making it secure as possible.

Tags are library specific not system wide. For example my work in progress library has people tags, my code archive has code related ones. by separating them like this the system does not get clogged up (actually I rarely use tags in OSX at all).

It also has the usual web clipping features, and can be automated via applescript and templates.

Your question did make me do a double take, for me the answer is I think that I just open an archive and it is categorised on screen how I want it, I do not use deeply nested folders, preferring tags, and these can be nested. For example I use a visual hierarchy, “@SOMETHING” capitalised and colour coded for top level tags and then sub tags off these, which I show in the file list sorted by tag. EagleFiler search is far faster than spotlight (again I never use this preferring launchbar) but this careful naming and tagging schema tends to make visual search in any one library enough.

I just “feel” organised, as I do with using OF. Of course I may not be who can really tell, but the good feeling I get is worth the $40 :)

Thanks for the thoughtful reply. I’ve never tried Eagle Filer but have experimented with DevonThink several times over the years and each time I end up opting for the native file system. I’ve used tagging quite a bit since mavericks, and I could see the value of hierarchical tagging, but for my use cases I have just fudged it with hyphenated tags (current, current-research, current-service, that kind of thing).

I’ve found that the combination of OmniFocus for managing my ongoing tasks and DevonThink for maintaining the long-term information about projects has worked well for me for several years. The fact that they both sync with a single mouse click or keypress means that the same information is available to me at work or on my laptop when at home or travelling. One of the things that I love about DevonThink is the fact that it will work with indexes to documents - meaning that I can keep all of my files on the filesystem (rather than ‘within’ DevonThink) but still have all the advantages of management and search that DevonThink brings.

OmniFocus works well for maintaining my daily list of things to be done (in order) - it’s fair to say that during my working day I pretty much live in the Forecast perspective. I make use of the notes field for maintaining details of my ongoing progress and also links to emails and documents that are associated with the project. But, like you, I feel that I would make more use of this field were it given more prominence in the UI. I general find that I work with the inline version of the notes field (the one that opens up under each task rather than the box in the bottom right hand corner of the UI). If it were possible to have this information available in a pop-up window or even to be able to resize the one in the bottom right hand corner that would be an improvement.

Just want to say that I love hearing about the way people use these tools and please keep it coming! My one issue is that I find it hard to visualize the systems. I have devonthink but I just can’t quite get my head around the ‘database’ metaphor in there. It would be great to see some sample databases. I’m going to look around but if anyone else wants to share specifics of their use case I’d love to see it!

I think the underlying thing here is it does not matter what you use barring some personal prejudices and needs, as long as you use something!

I have spent a fair bit of today clearing out and refamiliarising myself with nvALT which I use for notes and markdown code snippets in conjunction with simple note and a couple of Brett Terpstra command line tools, I have taken nvALT for granted, and glossed over how fast it is and how useful (for me).

I keep coming back to the realisation I do not really need to store much long term other than txt/markdown files, and my code work (again essentially txt files) plus a few images. I don’t use Word or Excell, and only have limited number of PDF’s. Most other files are transient, so in EagleFiler WIP archive they go until finished with.

This does not include accounting which as I have said goes in a secure EagleFiler archive, as does old e-mail. Really that’s about it Google search and a pininboard account handles web links I may want to save.

Sort of nvALTish, I thought I’d share that I have recently adopted Ulysses as my reference system. Since most of my reference is my own writing, I heart iCloud as my sync method, and it has some nice flows via URL scheme, I’m digging it.

But I get why many might not. Just thought I’d add it as an option.



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Yeah, I toyed with Ulysses as a note taking system recently but the absence of any way to link to particular documents on MacOS stopped me (and the iOS url scheme with non-human readable ids isn’t too friendly). nvALT is great for that on the Mac, but the links don’t work anywhere else. I’ve been on the Beta for a new app called Bear which looks pretty promising for x-platform note taking - v. responsive group of developers and active process with a launch anticipated in fall sometime.

@dfay Wow, that Bear does look nice! I think the thing that appeals to me about Ulysses (and which has me converting from iA Writer) is the note/sheet organization system. Interested to see how Bear handles that.

I’m not sure that I like the idea of subscribing to a sync service, though. Even so, this looks worth checking out. Thanks!


Haha if you don’t link proprietary sync then what are you doing with OmniGroup software? :) I believe Bear is going to use iCloud. For now there’s no sync for Bear for Mac bc it’s being distributed outside the App Store, but the iOS versions are syncing. Sadly, I’m not in the iOS beta yet.

Oh haha I meant “subscribing” as in “paying for on a recurring basis”. I’m not sure about how that revenue model sits for me.

Still, looking forward to checking it out.


Subscription is the new normal now.

The subscription model does take some getting used to. It’s something that has been introduced in the past few years substituting the pay-for-it-once model. I think of other things in my life as a subscription model. I can think of my cellphone, water, power, and gas as a kind of subscription model.

MIcrosoft office 365, Adobe creative suite, Hulu, Netflix, and FileMaker are a few subscription services that I can name off the top of my head. I believe todoist is also a subscription service as well.

I’m slowly learning to begrudgingly accept the subscription model as a way of life with my software purchases. Sigh.

As pervasive as it is becoming, I don’t think it’s normal yet.

Subscribing to a service is nothing new (TV, Internet, mobile phone), so Netflix makes sense - there is something “new” all the time as part of my subscription. But software is still trying to break in to this model. Look at the pains and public flogging that Smile took over going subscription for TextExpander.

Established high end software can make an easier case, I think - if it costs $1,500 and you’re probably going to buy a new version every two years, a monthly cost as a subscription is actually more convenient/cost-effective.

With less established software, though, I take pause: do I want to make myself reliant on a service with zero track record? I think about what Disney is doing with Infinity or that home security device system (who name eludes me) that just stopped working because the company folded. These services can simply go away if the company decides so or shuts its doors or gets bought up by a larger organization. Microsoft being subscription is one thing, but fresh new startup is another.

Whether this becomes normal enough, I think, is up to consumers as a collective: if we buy in, it will happen. If we don’t, it can’t work.

Anyways, just my two cents. Maybe I’m just an old curmudgeon who remembers paying hundreds of dollars for good software and liked the knowledge that that software was mine.