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Old Apr 5, 2009, 07:22 PM   #1
cricketbird
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Looking for good note taking software for research

I've looked at OmniOutliner, Yojimbo, Evernote, Scrivener and Zotero. I use and love Zotero and Evernote for other purposes, but they don't quite do what I want to do for research. I can't be that weird - I imagine there's a lot of folks in academia with similar interests.

I want to read research articles and take notes on them. But, then later, I want each individual note to be organizable into my paper flow but still linked to the reference they are from. That's the catch - all the above allow you to organize notes under the item, but then you can't rearrange them independently of that structure.

For example, say I have two articles:
Article 1
  • Note A
  • Note B
  • Note C

Article 2
  • Note D
  • Note E
  • Note F

I want to be able to drag my notes (each line a separate note) into my writing outline.

Topic 1
  • Note B
  • Note D

Topic 2
  • Note A
  • Note C

In all programs I've tried, rearranging the sub-notes is either impossible (Zotero) or loses the original reference (the others).

One way is to use Evernote's tagging features, but this requires entering the tag every single time. I'd really like to just take sequential notes from a single reference by entering the reference information, and then, every time I hit "enter", it creates a new note linked to that reference, but independently movable.

Any ideas?

Last edited by cricketbird; Apr 5, 2009 at 09:57 PM. Reason: made it less confusing
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Old Apr 5, 2009, 09:35 PM   #2
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Quote:
Originally Posted by cricketbird View Post
I've looked at OmniOutliner, Yojimbo, Evernote, Scrivener and Zotero. I use and love Zotero and Evernote for other purposes, but they don't quite do what I want to do for research. I can't be that weird - I imagine there's a lot of folks in academia with similar interests.
[snipped needlessly quoted text]
If I understood it correctly, you're looking for something very specific. Have you tried DEVONThink?

Look these posts here: http://parezcoydigo.wordpress.com/20...on-devonthink/

I don't know if you have already looked here (http://homepage.mac.com/kvmagruder/h.../workflow.html) and here (http://homepage.mac.com/kvmagruder/h...demicApps.html). Perhaps you can get some ideas.

Last edited by yellow; Jun 5, 2009 at 03:48 PM. Reason: Removed large quote
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Old Apr 6, 2009, 08:12 AM   #3
cricketbird
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Thanks

Thanks for the links - very interesting to see someone describe their workflow in such detail. I looked at DevonThink and it's still not quite as intuitive, and that workflow is frankly too much work. I just want to open a program, enter the reference (or copy it from somewhere), take some notes, and then sort those notes. I've re-taken a look at Scrivener and it's not as easy to do, but it's got the fewest steps of anyone and it's got that great corkboard layout.

Thanks again for the helpful information

CB
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Old May 19, 2009, 02:36 PM   #4
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Quote:
Originally Posted by cricketbird View Post
I've looked at OmniOutliner, Yojimbo, Evernote, Scrivener and Zotero. I use and love Zotero and Evernote for other purposes, but they don't quite do what I want to do for research. I can't be that weird - I imagine there's a lot of folks in academia with similar interests.
I've been trying for who knows how long to answer exactly the same question you pose. It seems like the simplest, most obvious need -- a basic replication of the old index-card system -- and yet I haven't found any software that meets it. I've been trying to learn DevonThink but find the documentation very difficult, and the whole program burdened with too much firepower. Have you discovered a better solution since your original post in April?

Last edited by yellow; Jun 5, 2009 at 03:48 PM. Reason: Removed large quote
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Old May 19, 2009, 03:36 PM   #5
jjvdhoef
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I've been looking for something like this to. The frustrating thing is that MS onenote actually is pretty close to this. But alas, that's not in the Mac office suite ofcourse.
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Old May 19, 2009, 04:04 PM   #6
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Perhaps Tinderbox is the solution you are looking for. It is described as the "tool for notes."

From the site:
Quote:
"Tinderbox maps your notes as you make them. Build relationships by arranging notes, organizing them with shape and color, linking them. Tinderbox lets you record ideas quickly and keep them where you'll find them again when you need them."
I have the demo, and am beginning to see what it can do. Take a look at some of the comments and application of the app. It has more horsepower than you need, but can grow as you grow your needs.
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Old May 19, 2009, 07:14 PM   #7
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You can also try out a mind mapping tool like FreeMind - in which branches can be moved (keeping structure). For writing papers, you can export to OpenOffice document -- use the free OpenOffice or convert from there to MS office .doc formats. A couple of conversion steps are needed -- but if nothing else works, it is worth giving it a try (it has its own limitations).
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Old May 20, 2009, 01:48 AM   #8
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I've got the demos of Mindola's SuperNotecard and Eastgate's Tinderbox. SuperNotecard seems to do the basics of what I want in a reasonably simple way. It could be a little more elegant and keyboard-centric, and seems to want a little more front-end organization (when what I'm looking for is data dump and back-end organization), but the basics are there and the price ($29) is not too steep. You can set the layout and views to be pretty much what I want. The biggest downside is that there's not an easy workflow I can see to link it to Zotero, which is sad. However, it's the best I've found and I can't procrastinate on my work any more - time to bite the bullet and make a choice.

According to the reviews I've read, Tinderbox is Da Bomb of notetaking, note organizing software, but at $229(!!!!) and my student budget, it's not under consideration. Also, I played around with it and it seems to suffer from insane feature bloat. I'm as nerdy as the next geek, but I don't really need the ability to program my notetaking software. I'm looking for something that just works, works well, and is easy and intuitive.

DevonThink was available for free a while back from MacHeist and has lots of excellent reviews where people have used it for organizing their files and notes. I didn't give it as thorough a go as I could have, but it still seemed to suffer from that problem of separating notes and references. However, it apparently has powerful automatic linking capabilities that people have used to data-dump in, and then have the software do a bunch of organizing automatically. I think I'll give it one more go before I plunk over the $ for SuperNotecard.

So, I'm using:
Zotero to organize my references - absolutely fantastic program, so easy to use and get references in (just click the title bar when you are on a journal site and it sucks in the metadata and the PDF, and if you set it up to do so, indexes the text of the PDF for super-awesome search capabilities, has a Word/OO plug-in, syncs to the cloud, remembers library proxies, etc. )

Evernote to organize my clippings and notes

Dropbox to keep my important files synced to the cloud and across work/home computers

Scrivener to do my writing (and, at the end for final formatting, M$Word)

And now, I think I'm probably going to start using SuperNotecard for my layout and organizing. Maybe DevonThink if I can get over its un-intuitiveness.
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Old May 22, 2009, 12:16 PM   #9
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Let's keep looking....

Thanks for the replies, Cricketbird and others. I'm trying again with DevonThink. If anyone catches onto something that fits the need for notes-coupled-with-citations, I'd sure appreciate knowing about it.
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Old May 26, 2009, 09:50 AM   #10
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same situation

I'm in the same situation. I have spent the last week reading reviews for every possible software, but it's hard to find reviews from an academic point of view. After reading everything, I have limited my options and installed demo versions of DevonThink, Scrivener, Journler, and now after reading this, SuperNoteCard and Tinderbox (thought after reading about it's price tag, I don't think I'll even bother trying it...)
I've read good reviews for all of them, but this was the first time I saw the issue addressed from exactly the right perspective. Perhaps because I'm spoiled by Zotero, when I begun my research, I was hopping to find an intuitive open source alternative for doing this, but I guess I was wrong. They used to make a program called Scribe exactly for this purpose, but they have officially abandoned the project, saying that Zotero covers the job of note taking suficiently, which it doesn't.
I think it's important to keep this thread alive for other people that are facing the same problem. I'll post my impressions after I try out the softwares I mentioned.
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Old May 26, 2009, 10:19 AM   #11
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I'm not sure it will do exactly what you're asking but have you tried "Notebook' from Circus Ponies? It is a pretty incredible note taking application.
Another to look at is VooDooPad.
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Old May 26, 2009, 10:25 AM   #12
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Pages '09 Dynamic Outlining feature?

You can drag and reorder bullet points as needed.
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Old May 27, 2009, 02:17 AM   #13
cricketbird
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Thinking about this more, a database program such as Bento, (free!) OpenOffice Base, or Filemaker Pro (or, if you still have the old AppleWorks, it's database software) might do the trick.

I think Bento sounds promising, but I'm still on Tiger. Could maybe one of you Leopard folks run the demo and let me know how it works for this purpose? Maybe it'll be an excuse to upgrade

In the meantime, having found nothing at hand that I like and needing to get to work, I've reverted to pencil, cards, and postit flags and have found it actually to be quite workable. I like the increased ability to easily draw sketches and such, and sketching out figures (instead of copy-paste) makes me see more "stuff" in the data. The low-tech option sometimes works well. Just wish there was a faster "search" feature than flip-flip-flip. But it gives me the opportunity to re-read my notes more often. I am doing this with the idea that when the right tool comes along, I'll just migrate back to the digital age, but maybe not...

I think one reason this is so hard, is that "taking notes" means so many different things to different people. It's hard to separate:
  • Taking notes in class / meetings
  • Clipping and storing info off the web
  • Taking research notes
  • Organizing research notes
from one another. For instance, grimreaper's recommendation of a word processing program and gerabbi's recommendation of Circus Ponies' Notebook are two excellent ways to take notes in class or a meeting, but are useless for organizing research notes that need to stay linked to a reference, be tagged, etc.

Evernote, Yojimbo, and their ilk are good at making notes searchable and accessible (via tags, folders, etc.), but not so good for keeping related reference info together with the note, or organizing notes into a writing "flow".

Zotero is great at keeping notes linked to their reference, but lousy at organizing them (except in alphabetical or date order).

Scrivener has the most potential I think, as it is actually designed to do just what we want. However, it's tagging is a little clunky, there's no batch change of cards (so that you can apply the same reference to a bunch of notes you just took). It's ALMOST there, but just far enough out of reach that I'm not using it.

Supernotecard was also quite good, but it just didn't play well with any other programs. The premise is top-notch though, and the closest I've found besides Scrivener.

Maybe after I graduate/drop out/fade away from grad school, I'll pull out my dusty old programmers hat again and see if I can whip up something. Any programmers out there whose skills were not last seen in the 1990s want to tackle this????

Last edited by yellow; Jun 5, 2009 at 03:49 PM. Reason: Merged Contiguous Posts
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Old May 27, 2009, 11:43 PM   #14
FlyingBarney
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Quote:
Originally Posted by cricketbird View Post
I've got the demos of Mindola's SuperNotecard and Eastgate's Tinderbox. SuperNotecard seems to do the basics of what I want in a reasonably simple way. It could be a little more elegant and keyboard-centric, and seems to want a little more front-end organization (when what I'm looking for is data dump and back-end organization), but the basics are there and the price ($29) is not too steep. You can set the layout and views to be pretty much what I want. The biggest downside is that there's not an easy workflow I can see to link it to Zotero, which is sad. However, it's the best I've found and I can't procrastinate on my work any more - time to bite the bullet and make a choice.

According to the reviews I've read, Tinderbox is Da Bomb of notetaking, note organizing software, but at $229(!!!!) and my student budget, it's not under consideration. Also, I played around with it and it seems to suffer from insane feature bloat. I'm as nerdy as the next geek, but I don't really need the ability to program my notetaking software. I'm looking for something that just works, works well, and is easy and intuitive.

DevonThink was available for free a while back from MacHeist and has lots of excellent reviews where people have used it for organizing their files and notes. I didn't give it as thorough a go as I could have, but it still seemed to suffer from that problem of separating notes and references. However, it apparently has powerful automatic linking capabilities that people have used to data-dump in, and then have the software do a bunch of organizing automatically. I think I'll give it one more go before I plunk over the $ for SuperNotecard.

So, I'm using:
Zotero to organize my references - absolutely fantastic program, so easy to use and get references in (just click the title bar when you are on a journal site and it sucks in the metadata and the PDF, and if you set it up to do so, indexes the text of the PDF for super-awesome search capabilities, has a Word/OO plug-in, syncs to the cloud, remembers library proxies, etc. )

Evernote to organize my clippings and notes

Dropbox to keep my important files synced to the cloud and across work/home computers

Scrivener to do my writing (and, at the end for final formatting, M$Word)

And now, I think I'm probably going to start using SuperNotecard for my layout and organizing. Maybe DevonThink if I can get over its un-intuitiveness.
I have been using DEVONThink for quite some time now, and absolutely love it. For me personally, there was no adjustment time, because I moved to it from a PC and from similar programs there (TreePad). While the program is loaded with features, I certainly don't use them all right now.

One of the benefits is that when I asked them for an academic discount, describing the work I do, they sent me a free copy. And now, after a major upgrade to v2 (to work with Leopard), they sent me another free copy. Which is very nice of them.
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Old Jun 5, 2009, 03:44 PM   #15
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some options

so, i've downloaded and watched/done the tutorials for devonthink, journler, and scrivener. i think none of them is exactly what i'm looking for.

the main problem with devonthink is that it isn't made to manage little bits of information, like cards with one single quote or idea, but rather documents in general (of any kind). it's certainly an impressive program, but it's overkill for me. first of all, i'm not looking for a documents manager, i would like to continue to use zotero to manage my references. it's AI functions would come in handy, but that's not my main concern. i'm looking for something that can help with the middle ground, after i have my references in zotero, and before i have a first draft to work in neooffice, pages or word. also, it's a very heavy and expensive application.

journler is great for taking notes in class, but it also is clearly not designed for research notes. scrivener is the one that gets closest to what i'm looking for, being organized around the idea of index cards. there are two problems, however. the first is that it is clearly designed thinking of index cards as chunks of writing, and not simple notes (single ideas or quotes). the second is that it is completely oriented towards a single project. i would like to use the notes i did for a book in different papers, and eventually dissertation chapters, and scrivener doesn't seem like it can manage the load.

what i'm looking for is a piece of software that will allow me to take a book or article i already have in zotero, and take notes in the following style:

BOOK 1:
A p. 121 "generic quote"
B p. 123 - a paraphrase or idea of what the author is talking about

BOOK 2:
C p. 13 "generic quote"
D p. 15 "generic quote"

afterwards, i should be able to access this information and rearrange it into papers:

PAPER 1:
- B (idea from book 1)
- a new idea
- D (quote from book 2)

and in the end, export this first draft to a word processor to finish my writing and format it.

of course, after i finished my area exams and courses, i will have more than a hundred annotated books, that i will want to use to write my chapters and my dissertation. that's why it's so important for me to settle on one program and stick with it. tagging and cross-referencing would be crucial at this point. arguably, any of the two software could be twisted and used for this purpose, but clearly that's not what they are designed for. there MUST be some kind of software to do this kind of work, it's really not that complicated, and there should be thousands of people in the same situation.

in the end, if i don't find a better solution, i will probably settle for devonthink, just because i trust it better to manage this amount of information. i just find the whole logic behind it quite old in terms of software architecture...
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Old Jun 6, 2009, 05:32 PM   #16
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Quote:
Originally Posted by marcosdavi View Post

the main problem with devonthink is that it isn't made to manage little bits of information, like cards with one single quote or idea, but rather documents in general (of any kind). it's certainly an impressive program, but it's overkill for me. first of all, i'm not looking for a documents manager, i would like to continue to use zotero to manage my references. it's AI functions would come in handy, but that's not my main concern. i'm looking for something that can help with the middle ground, after i have my references in zotero, and before i have a first draft to work in neooffice, pages or word. also, it's a very heavy and expensive application.

...

BOOK 1:
A p. 121 "generic quote"
B p. 123 - a paraphrase or idea of what the author is talking about

BOOK 2:
C p. 13 "generic quote"
D p. 15 "generic quote"

afterwards, i should be able to access this information and rearrange it into papers:

PAPER 1:
- B (idea from book 1)
- a new idea
- D (quote from book 2)

and in the end, export this first draft to a word processor to finish my writing and format it.
Actually, DT is designed to work very well with what you've described here. Some, like Steven Johnson, suggest the program is at its strongest with bits of text no longer than 500 words. Yes, it is possible to dump tons of whole documents into DT and have the program manage them. But, the program also works as an excellent note-taker for exactly the type of "small bits" you want to work with. All one must do is add a new rtf note. Put those notes in files that are descriptive of your sources. There are also a few scripts for adding notes that are impressive.

The note tree provides structure to the system, but DT databases are not bound by that structure. It is also very easy to put a short reference or reference code into any note. Furthermore, it is very easy to link notes together to concept notes or thematic entries-- of any size text entry.

The key isn't to watch a web tutorial that is produced for a much broader audience than your particularities, but rather to download and work with the program.

I would also suggest that DT is not only more efficient than flipping through your pencil and paper notes (assuming you're at least a moderately good typist), but the search capacities will quickly outstrip you personal memory capacity once your database moves beyond a handful of sources and notes. The AI infrastructure is akin to the difference between Web 2.0 and the Semantic Web. The AI is more flexible and powerful than a tag-dependent categorization, though the use of tags can help in refining document and concept similarities.

Finally, having all of your notes in moveable and re-arrangeable files, that can easily be plugged into new databases later on or replicated with a simple keystroke means your post-doc career will be more efficient and productive as well. Research doesn't begin and end ABD.

All that said-- tools are stronger when they are able to do specific things very well. There is nothing worse than bloatware that tries to do too much. You'll be much better off in dissertating if your research tools are very attuned to specific tasks. DT and Scrivener work very well together for specific points in the research and write-up process. Zotero is very good at scraping metadata from the web. Together, the three provide the ability to add real computing power to the ponderous old school systems of humanities tradition.
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Old Jun 7, 2009, 12:24 AM   #17
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Old Jun 22, 2009, 12:05 PM   #18
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FlyingBarney and v.m.,

Thanks for your posts. I'm interested, and have DevonThink, but I'm still not sure how to use it even after looking at the help and reading at the links you posted.

Can you share HOW you use DevonThink for academic writing? I'm intrigued by its "intelligence", but I can't figure out how you:
(a) take notes about a PDF file (ie, the notes are somehow permanently linked to the PDF file, not just in a folder together with the PDF)
(b) organize notes - they seem determined to stay in their own alphabetical order

Thanks,
CB
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Old Jun 23, 2009, 11:23 AM   #19
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What about Curio?
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Old Jun 24, 2009, 12:38 AM   #20
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Curio is awesome and I just bought a license for it this morning! I'm using it for brainstorming and project planning and am finding it absolutely fabulous. Just the mind-mapping alone moved my writing forward by a huge jump over the weekend and inspired several new research project ideas. The way that dates in to-do lists are automatically filled in is a life-saver, and the ability to spread ideas in many forms (text, photo, scribble, files) across a white-board is incredibly helpful for guiding my thinking and writing.

However, it doesn't do any better than the others here for organizing research notes. It doesn't keep the notes linked to the PDF if you rearrange the notes. It doesn't have a field for saving the reference info. So, it's valuable, but still not quite what we academics are looking for.

Thanks though
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Old Jun 24, 2009, 01:01 AM   #21
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I use Papers to search for and organize the articles I read. It assigns a unique bibtex citekey to each paper. When I drag a listed paper into another program, the citekey is dragged with it, so it is easy to find later. I then take notes in a separate program and reference by citekey. Yeah, it's not automatic, but it works for me. The advantage of using Papers is it's stupidly easy to find the articles you're looking for, instead of digging through a bunch of PDF files.

I like Voodoo Pad for taking notes (it's like a personal wiki), but from what you've described I think you would like OmniOutliner. You could use it both for storing notes and writing outlines, and I believe you can link to files directly and rearrange points at will.

--
One other suggestion: Have you tried Skim? It's a nice PDF reader that lets you highlight and take in-line notes. And it's free
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Old Jul 5, 2009, 05:09 PM   #22
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Same Problem

I've got the same issue as cricketbird. I'm tempted by Scrivener, DevonThink and OmniOutliner, but none does what we are looking for in terms of organizing research notes. Are we misreading the specs?
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Old Jul 5, 2009, 05:11 PM   #23
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Curio is def. the best all around application. I used to use MindNode Pro and then Word's Notebook feature. Although I like a good ole' spiral.
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Old Jul 5, 2009, 07:39 PM   #24
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Curio

Doesn't Curio duplicate some of Inspiration 8.0 functionality? I have been using that for concept mapping.
I just downloaded DevonNote and like it quite a bit. It won't accept .pdfs, though. I'm guessing you have to download DevonThink to organize .pdfs.
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Old Jul 6, 2009, 06:01 AM   #25
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I've gone with Scrivener, less complicated than Devonthinkpro . I like it so far. I was out of my comfort zone in terms of what it had installed. A 91 mb plug-in, icon in the menu bar, and a tray on the side of the screen. Too much for me, I deleted it.
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