Disclosure: Below is a long read due to me having given a lot of thought to how I want my system to work.

A little background to my problem. I'm currently an undergrad student who's in their sophomore years. I have begun to recently dive deeper into scientific literature (mainly to do with neuroscience and behavior) and am taking notes. I have a system I use to gather info and then read and analyze what I have gathered and I consider this system to suit my need. But when it comes to the note-taking part I have yet to find something that does work. The needs I have are for some rudimentary formatting (bullet and number list with multi-indent capabilities), images are a must (I include figures from papers in my notes, or make concept maps or diagrams to further my understanding). I also really want the ability to export my notes easily in case the software I ever work with is shut down for some reason and I need to move my data into another one. The last needed capability is the "anytime, anywhere" functionality where I can access it form any computer or device (like my iPad) and edit the info. Extra capabilities that would be appreciated is the ability to make tables or include mathematical functions, or inking.

I tried Dokuwiki which I enjoy due to the wiki linking concept. But my problem is that maintenance of this wiki is troublesome and any markup besides text formatting is incredibly complex. Considering that I encounter things where I might make tables or include mathematical functions, I struggle to do the same in Dokuwiki. Also, even just getting images into Dokuwiki can be a chore as there's no drag and drop or copy and paste and I have to use the media manager. I also need to be able to access the internet if I want to access my notes (I have it running as a website instead of a local right now since I want to be able to access it on my desktop, iPad, and school computers). Though this does have the bonus of being open-source and having a strong community and text file storage system so I know that my data would be safe in there for a while.

So the temporary solution I have come up with is Onenote. It allows me to do everything I mention in the first paragraph except for one of the most important thing....exporting features. While I could get my info out in multiple formats right now, I am concerned about how most of these formats require proprietary software to edit (like Onenote or Microsoft word) or isn't really editable (like pdf and mht output). These formats also make it harder to import into other software unlike txt. (which Dokuwiki can do) or rtf files. Searching is also a little weak compare to others I have tired (Evernote allows tag and full text at the same time, ConnectedText has Boolean).

I have also tested Evernote (same export problems), ConnectedText (I can't really use it on my iPad), Resophnotes/ Simplenote (no images).

So my main concern is does anybody know how to get data out of noenote into another thing easily (or at least not make it torture) or an alternate software I haven't tried yet that does fulfill my needs. Also, if you use Onenote, I would appreciate a case study example just for reference on how I can improve my system.

There was a similar discussion here a while ago, though I can't remember if OneNote was specifically discussed:

http://www.outlinersoftware.com/topics/viewt/3436/

Regarding CT on iPad, apparently there is a way (though I haven't tried it):

http://takingnotenow.blogspot.co.uk/2011/10/connectetext-on-ipod.html

If you don't have time to read the whole thread, here is the system I came up with as a result of that discussion (but it's mostly text based, as I don't need to capture images all that often):

http://www.outlinersoftware.com/topics/viewt/3436/35

If you read a lot a of scietific literature, which I presume most is in pdf, I can suggest my setup:

pdf xchange viewer - allows notetaking, highlighling etc. I also use my own tags like "mystop", "mynote: ...", "mytodo: ..." etc to mark what has to be done, where i stopped reading, etc
archivarius, dtsearch or similar for quick finding of what you need to find in 100s of articles/books + your own tags
a pdf comment collector - tool to collect your pdf notes into one doc - this is tool i helped to develop, i use it to go quickly over my notes in pdf files. I also use colour coding, the initial notes are yellow, those processes and stored in Ultra Recall are grey - easy to go through them by colour in pdf exchange viewer
Ultra Recall - to store all my important notes, pictures (in my case math formulas) etc, it's all indexed so fast to find what i need

ps: the above setup helped me to get a phd in math, and i still use it on a daily basis in my job

In fact, tags do still exist in OneNote, although they appear to have been deprecated. I use them myself (you can customise the ribbon and insert various tag-related commands into any tab you like; you'll have to create a "custom group" first - oh, and it's worth mentioning I'm using OneNote 2010: earlier versions can't be customised as easily). This adds some flexibility to OneNote, although you won't necessarily find it carries over to any mobile versions you use (I also use iOS and Android versions of OneNote, both Microsoft's and other clients such as MobileNoter and Outline+).

But you may be amused to hear that you can copy and paste OneNote pages into MyInfo very easily - tables are copied over in usable form, a few less significant things (e.g. checkboxes) are lost. MyInfo is a whole lot more useful for search operations than OneNote is! Mind you, you might then quite reasonably ask: why not simply use MyInfo instead?

I like Quant's suggestion of using a powerful PDF editor (like PDF Xchange Viewer, which is amazingly good). This would also allow you to manage your OneNote data on a mobile device: the number of high-quality PDF editors/viewers available on iOS, for example, is really quite spectacular, and many of them (e.g. iAnnotate, PDF Expert Pro) allow you to insert/delete pages, write notes into the file, highlight/draw etc. and even change text (depending on permissions etc.). So you can export a whole bunch of OneNote material into PDF format, then play around with it in a suitable editor. Again, the search options in various PDF viewers (not least Acrobat Reader) are generally superior to OneNote itself.

PDF is a very useful format for gathering/analysing info, even if it's generally regarded as less flexible. It's very robust, comments/annotations can be exported, you can read it on more or less any platform. You can copy text out of it. Really not to be underestimated, even though most of us instinctively prefer "low-end" alternatives such as raw text!

Another alternative you could consider is SilverNote, which is currently in beta but looking very promising. Nice support for images, tables, drawings etc. And a nice, responsive developer, too! And the very latest version has a hugely improved and very powerful search function. You'll find a (free) version at www.silver-note.com - I'm just about to write and compliment Adam on the lovely integration of general search with intra-note search, and the way search results now allow you to scroll to hits.

Deffo worth a look - in many ways Silvernote is a kind of alternative OneNote, with plenty of options for dropping stuff anywhere in the page. The table function is still a bit basic, but shows promise!

Cheers,
Bill

Sorry if I take long to respond, I'll be busy till Friday afternoon when I'm finally free from the curse of midterms!

Dr. A

Wow how did I not find that thread? Thank you so much, it's proving to be an educational read. Your system is actually very similar to yours. I also use PDF Expert and export the notes into an email and then make little corrections (expand upon thoughts, paraphrasing, organizing into sections like methods, result, etc.) after pasting into Onenote. The only difference is that I have a to read folder in my Dropbox that I move PDFs into when I want to read them later and move them back into Mendeley (my current PDF manager of choice) when I'm done. The Dragon dictation thing is very interesting though and I'll have to try that sometimes and hope my accent doesn't hinder me. As for the iPad workaround, the unfortunate thing is that it requires internet. The reason this concerns me is that if I ever do something like Doctors without Border or work in rural areas (something I am considering), then I'll lack internet access the majority of the time (why I rejected Dokuwiki and ConnectedText). So I wanted something that has a native client on the iPad (I'm using Outline+ right now for Onenote usage on iPad).

Quant

Yeah, the majority of my info are in PDF (for web articles/ blogs I use Joliprint to convert them into PDFs, only other file format is MP3/ MP4 for podcast and TED talks I take notes from). I use Nitro PDF instead because I was already use to it and it provides me with most things I need (basic annotation, and can print things to PDF, though web pages are iffy for selectable text, see Joliprint instead for that). Color coding is something I'm considering, I might use the system suggested here for color coding (http://drosophiliac.com/an-academic-notetaking-workflow.html I haven't tried Ultra Recall yet, can you give me a run down vs. Onenote?

MadaboutDana
I do use tagging in Onenote, though more for exam studying purpose (tag summary of maybe everything I tagged in my bio notes with the vocab tag). The problem is that unlike tagging in Evernote, you can't search two tags at once (as far as I know), which is kind of the purpose of tagging in the first place (having things under different categories without having to make a separate "folder" for each of them). The tag summaries does exactly that, which is helpful for exam review, but not for finding things that are related to say prefrontal cortext and perception at the same time.

I'm not sure I would ever need to export my Onenote into PDF (unless I wanted to share just one page instead of a whole notebook through Skydrive). I can do all the things in a PDF editor that I can do in Onenote except for drawing (I just draw on the iPad and then put it into Dropbox and copy and paste it into Onenote). I could export all my stuff into PDF if I ever just wanted to get my data out of Onenote immediately and then copy and paste from PDF into another program. But the reason I wanted to export to txt or rtf was that if I ever move from Onenote to another program later on, it would be easier if I had it in a common file extension that could be imported widely (like txt or rtf). But yes, PDF is a very future-proof option right now and might be what I do if I ever wanted to get my data out of Onenote fast. Since I could still edit the text in my file and just index my files. Though my Wiki-links wouldn't work which would make me slightly sad (part of the reason why I like ConnectedText so much).

Silvernote seems really interesting. Though to me it just seems like a free version of Onenote which I don't need since I already have Microsoft Office for free through my school. The drawing part seems interesting (instead of me drawing a concept map outside of Onenote on LucidChart or using Dia and then copying the image in) but the search is what I really like. I'm still not sure why Onenote doesn't have searching as good as Silvernote. Though I'm not sure if I'll ever really need the searching since my notes are pretty organized in notebooks (wiki-links help too) and stuff so I can find things rather easy. It's just the tag summary that doesn't allow two tags that annoys me.

Everybody,

Thank you for all the suggestion and insight so far, they have been incredibly helpful and gave me some things to check out.

Also forgot to mention that I might check out MyInfo too. But my main concern is that I have something that will work no matter where I go whether it's on my iPad without internet access or a computer that only works on Ethernet but can't install desktop software so only a web client I can use. This is why I have settled on Onenote (though Evernote could do the "anytime, anywhere" job too) so far.

Glad you found the thread useful. I would still think that some sort of a desktop wiki that also works on iPad might be a solution. You may want to dig around Manfred's blog (http://takingnotenow.blogspot.co.uk/ a bit because he's covered a lot of different wikis and mark-down apps. There are also quite a few websites out there that compare every imaginable wiki under the sun.

Why do I think a wiki would be good? 1) Because text files in the end are still more versatile and more likely to survive than PDFs, and 2) because of the distinction I would make between your "brain" and your "library."

Your "brain" is the software that contain your notes and your analysis of items in the "library" (or multiple "libraries"). The "library" should be external to your "brain," otherwise it will clutter it with irrelevant material. A wiki is good for a "brain" because it can create connections like a brain (i.e. not necessarily in a hierarchical tree-like order) and can hold a large number of text notes organised in multiple ways, and can also link to external library items.

So I'd keep notes (such as the ones you take after reading a PDF article) in the wiki ("brain"), however I'd leave the PDF article in the library. Chances are you may never ever need to look at that PDF again, if you had taken good notes or if it turns out to be an unimportant or poor article. You only want to end up with the good stuff in the brain, so you can make sense of it, find it more easily, remember it, do things with it.

Then it just becomes a matter of syncing your brain across your devices (desktop to iPad), and keeping your PDF, image, website clippings etc. libraries synced across your devices. The latter could be in one or multiple apps (there are advantages and disadvantages either way). Basically it's a good idea to keep your own notes and the stuff they derive from or refer to separately, to avoid duplication and to maintain clarity.

I do agree with what you say about tagging - and also about cross-platform. There's a huge opportunity here for somebody to produce a really powerful cross-platform app that combines the strengths of a OneNote/Silvernote, wiki and Curio (I love Curio - it's just a shame I haven't got a Mac!).

An app I use a lot (because it's very flexible and also supports and indexes third-party files) is Alfons Schmid's Notebooks - originally for iOS but now also available in beta for Mac and Windows (you'll probably have to ask Alfons if you can join the Windows beta program, which doesn't currently appear on his website). I've actually returned to Notebooks for most of my iPad-based text management needs, simply because it's so flexible. It synchronises through Dropbox, each "book" is effectively a separate folder, and each "note" is effectively a separate file (HTML-based, as it happens, or else raw text) - hence the plural "Notebooks". It's actually very simple at heart, but also very powerful. And Alfons is very nice!

It doesn't sound as if you'd necessarily find Notebooks any more advantageous than Outline+ (which I also use, and have a great respect for), but you might like to take a look. It's an app that steadily grows on you (I'm also now using it for task/to-do management, after trying literally hundreds of alternatives!)

Cheers,
Bill

MadaboutDana wrote:

It doesn't sound as if you'd necessarily find Notebooks any
more advantageous than Outline+ (which I also use, and have a great respect for), but
you might like to take a look. It's an app that steadily grows on you (I'm also now using
it for task/to-do management, after trying literally hundreds of
alternatives!)

If and when you find the time, could you briefly describe how you use a note-oriented application for tak management? I have ended up doing the same thing with a simple .txt file --which I find quite ironic given the number of specialised applications that I have tried. I'm not really happy with it, but at least it doesn't get in the way and it's always available wherever I may find myself (via Dropbox and Android phone) which I find the two most important aspects. Ideally, you might want to start a separate thread.

Alexander Deliyannis wrote:

MadaboutDana wrote:
>It doesn't sound as if you'd necessarily find Notebooks any

>more advantageous than Outline+ (which I also use, and have a great respect for),
but
>you might like to take a look. It's an app that steadily grows on you (I'm also now
using
>it for task/to-do management, after trying literally hundreds of

>alternatives!)

If and when you find the time, could you briefly describe how you
use a note-oriented application for tak management? I have ended up doing the same
thing with a simple .txt file --which I find quite ironic given the number of
specialised applications that I have tried. I'm not really happy with it, but at least
it doesn't get in the way and it's always available wherever I may find myself (via
Dropbox and Android phone) which I find the two most important aspects. Ideally, you
might want to start a separate thread.

I'm obviously not MadAboutDana but it's important to distinguish note-oriented application from sticky note/cork board oriented application for task management.

One is simply removing the bullet point check boxes associated with to-do lists and framing it into a different box that resembles a column view/spreadsheet scale.

The other may or may not utilize file attachments to create image associations on a basic level but on a true scale may be more about note taking to create tasks instead of merely storing notes on them. An example philosophy might be to rereading ones' notes, find out what you did yesterday and then decide what you would do today. Very basic journal level stuff but it's extremely tricky when it comes to software/software methodology.

For .txt implementing folders (not meant for organization) is different from implementing straight .txt notes for example. Say a .txt being contained in a folder that contains parts of the same entry but with images and docs and spreadsheets for the same folder name/.txt name thus allowing for one entry to have different "views" rather than different "tags".

Sorry for taking so long to come back to this thread. I believe that for now I'll stick with Onenote since Microsoft has continued to develop it and I believe that it will become nice to use when they can come up with a metro version for the iPad. My concerns about future-proofing are not too bad since I know Microsoft will stick with Onenote for the foreseeable future. Because of that, I'm sticking with my system that I based off of Daniel's system for his Circus Ponies notebook. Where I have notes from my sources in one notebook then I have a topic notebook dedicated to specific topics (neuroanatomy, cognitive neuroscience, psychiatry, etc.).

However, if Onenote were to ever go to hell (very possible when it's Microsoft that's developing stuff), I would probably moved to a system of either Dokuwiki or ConnectedText since they both use plain text as the way to hold their files. Then with appropriate file naming for my images, and referencing to the file names in the text, I can create a fairly future proof system too. But as of right now, there's no good wiki that works on both iPad and my desktop without having to be connected to the internet all the time.

Forgot to include link, but here's Daniel's system for Circus Ponies notebook I was talking about:

http://www.organizingcreativity.com/2009/09/circus-ponies-notebook-for-academic-writing-eg-thesis-writing/
http://www.organizingcreativity.com/2009/09/circus-ponies-notebook-the-best-tool-for-structuring-creative-writing-projects-esp-research-projects/
http://www.organizingcreativity.com/2009/09/circus-ponies-notebook-and-scrivener-for-writing/

Also, if any of you are interested in comparing Wikis. When I first did my search, I used WikiMatrix (http://www.wikimatrix.org/ before deciding to test out both Dokuwiki and ConnectedText.

MadaboutDana wrote:

I like Quant's suggestion of using a powerful PDF editor
(like PDF Xchange Viewer, which is amazingly good).

I just had a bit of a problem with viewing a PDF in Firefox with the XChange Viewer (free version!), and this time I bothered to email the error report. I received a response in a matter of minutes from their support guy. Wow! Very impressed. The problem had nothing to do with XChange Viewer in the end. Excellent service.

Dr Andus wrote:

I just had a bit of a problem
with viewing a PDF in Firefox with the XChange Viewer (free version!), and this time I
bothered to email the error report. I received a response in a matter of minutes from
their support guy. Wow! Very impressed. The problem had nothing to do with XChange
Viewer in the end. Excellent service.

Glad to hear this. I've bought PDF XChange Pro from Tracker Software, which includes PDF Tools; in fact, you'll find that they cross-promote their products heavily, so what you end up paying is significanty less than the sum of the nominative prices.

Along with (free) PDFill tools provided by another company, I can do everything I've ever needed to do with PDF files, including some very sophisticated batch modifications for full books. In fact, for most people the free XChange Viewer plus the free PDFill should be more than enough.

I should add that I tested the full version of Adobe Acrobat and I foud that the same modifications were considerably more complex with it, while at the same time its price was almost 7 times what I paid for the XChange toolkit.

Yes, I'd agree with that. We've moved over to PDF Xchange Viewer as our main in-house software - very powerful, loads of lovely features, and the Pro version is very cheap. Acrobat is well over-priced for what it is, although I notice that Adobe is starting to emphasize the collaboration features more nowadays. But everybody can collaborate using PDFs in any case! I mean, I do a lot of my PDF markups on my iPad using iAnnotate or PDF Expert, for goodness sake! Both of which bear comparison with Acrobat.

Alexander Deliyannis wrote:

Dr Andus wrote:
>I just had a bit of a problem
>with viewing a PDF in Firefox with the XChange Viewer (free version!),
and this time I
>bothered to email the error report. I received a response in a matter
of minutes from
>their support guy. Wow! Very impressed. The problem had nothing to do
with XChange
>Viewer in the end. Excellent service.

Glad to hear this. I've bought PDF XChange Pro from Tracker Software,
which includes PDF Tools; in fact, you'll find that they cross-promote
their products heavily, so what you end up paying is significanty less
than the sum of the nominative prices.
I should add that I tested the full version of Adobe Acrobat and I foud
that the same modifications were considerably more complex with it,
while at the same time its price was almost 7 times what I paid for the
XChange toolkit.

Not an outliner, but since we'd discussed it and it's part of the eco-system: PDF-XChange Viewer PRO is 40% today (I caved in, after using the free version for years, and becoming frustrated with my old Adobe PRO 8 on Win7...)

http://www.bitsdujour.com/software/pdf-xchange-viewer-pro

I can definitely recommend it. With PDF Xchange Pro and the PDF Xchange Tools I do just about everything I would have needed Acrobat Pro for. Watch out for possible cross promotions; Tracker Software do quite a few for their customers and you may be abble to get the Tools with some significant discount as well.

Alexander Deliyannis wrote:

I can definitely recommend it. With PDF Xchange Pro and the PDF Xchange
Tools I do just about everything I would have needed Acrobat Pro for.
Watch out for possible cross promotions; Tracker Software do quite a few
for their customers and you may be abble to get the Tools with some
significant discount as well.

Looks like they now offer their PDF printer driver for free as well (which might not be a big deal if you're already using another free driver anyway - though this might give you some extra controls):

"PDF-XChange 'Lite' 2012 is a simplified version of the PDF-XChange Standard 2012 print driver"

http://www.tracker-software.com/product/pdf-xchange-lite

Dr Andus wrote:

Looks like they now offer their PDF printer driver for free as well
(which might not be a big deal if you're already using another free
driver anyway - though this might give you some extra controls):

In my experience, one can never have too many PDF printer drivers; each one has its own strengths and weaknesses, and there will always be a situation where one doesn't print as expected and another will provide the solution.