I am a PhD student writing a qualitative thesis (ca 250 pages with six main chapters) based on a range of (mainly textual) sources including interview transcripts, websites, notes, reference articles (primarily PDF), books, and the like. Scrivener (www.literatureandlatte.com) was recommended to me recently by a colleague and if I had a MAC I would jump at it. But like many others stuck with a PC (eg www.outlinersoftware.com/topics/viewt/1074 & www.badlanguage.net/i-want-scrivener-for-windows) I'm pulling my hair out searching for a Windows alternative. Scrivener's author, as some have already noted, offers several suggestions (www.literatureandlatte.com/links.html). But these, including PageFour (www.softwareforwriting.com), do not come close to Scrivener's slick interface in my view.

Next I became interested in PIM/GID (Personal Information Management/Get It Done) software. This post (www.outlinersoftware.com/topics/viewt/945/0/list-of-pims) offers a huge list of stuff but it's not reviewed and I don't have the time to go through each one and experiment. I'm impressed with Evernote (www.evernote.com) but I'm NOT thrilled with its synced online membership business model. The 'Premium' (monthly/yearly paid subscription) version offers PDF searching and indexing - a must in my view - but must I pay The Man for the rest of my career? The Brain (www.thebrain.com) and ConnectedText (www.connectedtext.com) are two runner ups but as someone else mentioned, Brain's price is a little high and I'm still not sure what I think about the mindmap style of organization (a bit too geeky). Meanwhile, ConnectedText's Win98-like interface, like so much of the PC stuff, doesn't really cut it aesthetically.

Before I hand over my money and my life to Evernote can anyone here come up with a wonderful solution to my dilemma? Again, I'm looking for a piece of software that I can 'dump' (link) all my sources in one place and enables the beautiful marriage between content and form, searching and sorting, referencing and drafting, culminating in a final text. Like Alexander screams, 'I want it all now!' (http://www.outlinersoftware.com/topics/viewt/879/0/i-want-it-all-now

Thanks for you thoughts.

Great forum by the way!!

I use Ultra Recall for purposes similar to yours It is extremely flexible. It is not primarily a writing tool, but you can make it one. Plus, it is very good with metadata which you will undoubtedly need to track your references. UR also indexes pdfs provided the file has text and not an image of the text. Files can be stored and/or linked within UR. UR can manage databases up to 2 TB. My largest is 16 GB and it works fine. The learning curve is perceived as steep, but I found it very logical.

As a writing tool, WhizFolders deserves a look. It does not handle pdfs in the way you specify.

Jon

Possibly too late, but Keith Blount's closing comment to his post in this thread on the Scrivener forum may be relevant: http://www.literatureandlatte.com/forum/viewtopic.php?f=15&t=6815

It's perhaps a pity that IdeaMason has shut up shop. It wasn't perfect, but it was designed to do most of what you want.

H

I definitely think you should at least look at Biblioscape. It seems to have been undergoing rapid development over the last year or two and has the potential to be what IdeaMason could never quite pull off. I used it happily until jumping ship for a mac last year. Actually, I'm curious to hear what people think of version 8.

Of course what you should really do is run away screaming from you Ph.D. program while you still have the chance, but that is another story.

God speed,

Matt

Peter, the problem with the PC world is that though it once boasted of having more software functionality than the Mac world, what it has in quantity doesn't equate to quality.

I would not think of paying Evernote as paying the man - the amount is reasonable, and the program offers a way to collect all sorts of material, and some ways to process it, although as I get older I find its grey on grey tag list, and the limited ability to work with tags, a pain in the butt.

There have also been repeated requests for EN developers to enhance the information management aspect of the program, which has been on hold for about two years as the program developed its cloud and multi-platform capabilities. In fact, to do that, developers actually removed information management features from EN for the PC, and have tested the loyalty of people doing heavy lifting with information in terms of getting those features back in.

Meanwhile, other programs provide those features, at least in terms of tagging and metadata. Like I said, it is hard to find a PC program where the developer seems to have covered all the bases.

However, on the plus side for EN: it captures all kind of material with great accuracy. I love that I can drag 'n drop PDF files into it.

And what does qualify EN as a writing tool for me is that I can have more than one note open at a time.

For writing, especially when using notes with quotes 'n stats it sure makes it easier if you can see both your data and the window you are writing in at the same time.

Surprisingly, programs such as UltraRecall and MyInfo have not thought of that.

A program that has is WhizFolders. It works with the outline metaphor, and may not be the best place to keep all your data. However it is great for writing, lets you have multiple notes open.

It also has a key word or tag system that supplements the nested folder approach that is part of the outline metaphor.

Zoot 5 will also work well for you - it has multiple open window capability, captures stuff reasonable well, etc.

The beta version, Zoot 6, is up to about its 50th build, and may be solid enough for you to use now - although as part of the beta testing process the developer asks that all data files in it be deleted.

Zoot may be the best example here of an information collector, information processor, and writing environment.

One of its long time users and advocates is James Fallows, national correspondent of The Atlantic Monthly. There used to be on the Zoot Yahoo Groups site a file with James' template for organizor research material for articles.

His articles, though well written and quite readable, are information and reference dense. He has found Zoot a good way to deal with a myriad of quotes 'n stats 'n facts that have to be woven together into an elegant work of enlightening prose.

Daly

Coincidentally, there was a reference to a Scrivener rip-off for Windows at the Literature and Latte site this morning. Here's the link:

http://www.storyboxsoftware.com/index.php

I have no idea if this application is stable or works, but just thought I'd point it out to you.

Steve Z.

Like many PC users, I have been waiting for a PC clone of Scrivener for a long time. I'll certainly test Storybox, and if it's even vaguely promising, I'll probably avail of the "early adopter" pricing just to encourage the developer.

Hi Peter,

As a fellow PhD student (although not yet at dissertation stage), I can relate to your quandary. I also know that, for myself, the software search can become a big distraction (a situation amplified by the fact that I have both an inherited Powerbook and a PC). So, I've tried them all (almost).

First off, I would point out that the current beta version of Zotero offers much of the same functionality as Evernote. Zotero gives you (something like) 300 MB of free storage, although I set up Zotero to use a WebDAV account through my university so that I can have more storage room. PDF's are automatically indexed (so long as they have text information---Zotero does not do OCR like Evernote). Zotero has rich-text notes and tagging as well. In the same vein, Mendeley offers much of the same functionality as Zotero, and they say they will support OCR soon.

However, neither of the products mentioned above serves very well as a serious writing/drafting environment, in my opinion. For me, the killer feature of Scrivener is the ability to view one's assembled chunks of text as an integrated draft and to edit that draft. So one can switch back and forth between working on the document as a whole and working on just one isolated section. I haven't found other programs that offer this. Whizfolders, for instance, has a combined *view*, but you can't edit in that view. Biblioscape tries to offer something similar but I found it still primitive and not really usable. IdeaMason isn't bad, but I find it frustrating that one can't just write directly in a draft (or "composition") -- one must take the time to create a new "Idea" first, which I find interrupts my ideational flow. I have not worked much with Ultra Recall or Zoot, so perhaps I should still give them another look. I just checked out StoryBox, and it's definitely not at a point where I'd use it yet, but it's a promising start.

Even though I have an (aging) Mac, I have not settled on Scrivener as a writing environment. It tries to be a combination of outliner and word processor, but I find that I can do my outlining much better in an actual outliner (I love OmniOutliner on the Mac; the free Ecco Pro is great on the PC, although I wish it could export OPML---InfoQube may do that). As for writing and drafting, I do some of it in the outliner and the rest in a word processor.

The moral of the story for me (although I don't profess to have cracked this particular nut) is that in the long run it makes more sense to use a combination of dedicated tools rather than a single integrated application. So, I use Zotero for references, notes, and PDFs; I use OmniOutliner (or Ecco Pro), as well as Cmap Tools for outlining and brainstorming and some drafting; and then I use a word processor for the final stage. (Another moral of the story for me is to stick as much as possible to tools that don't lock my data in a proprietary format.)

That said, I am still searching for software that would actually facilitate my writing process. What I would like is a program that would have an "Outline View" in which one could do one's writing in single-pane outliner mode, and a "Draft View" in which one could see the same text in regular page layout (including footnotes). I would like to be able to switch back and forth between seeing my text as it will actually look when I submit my paper, and seeing it in a hierarchical organization (which is how I actually conceive of it). Actually, good old Microsoft Word comes closest to this, if one converts all the heading styles to regular unformatted text, but since it's not designed to be used this way, it gets awkward. (Plus I want cloning and flexible text folding!) But now I'm veering off topic...

Good luck,
Lucas

What fantastic responses! Thank you!

Jon - On your suggestion I had another look at UR. It definitely has some nice features. However, unless I?m wrong (I only browsed the documentation) it only allows pdf importing but it lacks reference management (like Biblioscape or Endnote) for citation export. As you point out, it feels a more like a project management (admin) tool than a writing (creative) tool? but that?s probably unfair because it does seem to handle a lot. I especially like how hyperlinks can be created between different elements. But I am a bit worried by the apparent necessity of tweaking attribute to enjoy accurate search results down the line. WhizFolders was also recommended which looks great for creating a network of interlinked notes/ideas. However I?m looking for software that can do that but then also move me into the next stage of writing prose, argument development, etc.

Hugh, Stephen, JohnK - Thank you for the StoryBoard link. It looks like the closest thing to a PC Scrivener so far (until PC Scrivener comes out ;). However I think after all this current reflection I?m leaning more towards a PIM designed for writing research and not ?just? a writer?s program for story development. So far Evernote and Biblioscape both (in their own ways) imitate the workflow I have in mind. There seems little incentive to learn and use IdeaMason at this point since it is discontinued.

Matt ? your suggestion for Biblioscape pretty much hit the nail on the head. I haven?t started using it yet but the website provides a complete manual. However, at least two issues emerged for me. First, selecting pdf text (underlining) for hyerlinking notes didn?t look like it?s been implemented. I assume this means that one must manually preview the document (pdf) looking for the place of the note reference, unless of course the page number was included with the note. I have become accustomed to manually underlying and leaving scattered notes in my pdfs with Acrobat Pro but I was hoping to find a way to import, organize and search these in one place. Second, it doesn?t look like the process of creating notes on the fly is supported. Instead one has to stop and assign attributes, categorize it, and give it a name. With Scribener for instance one doesn?t have to interrupt the writing process but instead keep writing. Meanwhile, Evernote is still attractive simply because of its superior graphical interface in my view. Nevertheless I am still concerned about the risk of upload my project to the cloud so the search is not over yet. Re: PhD ?Running away screaming? - now that?s a great title!

Daly and Lucas ? Both of your reflections explore the nuances of my (our?) dilemma extremely well and are very helpful! I?m still a bit stumped, but at least the choices are now narrowed!

One more question - Are any of you concerned about ?cloud syncing? with software clients like Evernote, Mendeley, or Zotero? For instance, let alone the copyright issues, I have ethnically sensitive material and just the thought of it getting uploaded somewhere ?out there? weird?s me out a little.

Rather than respond any further I think I?ll pause here and let the others jump in? ;)

Thank you again!

That darn cut and paste - I just found out the hard way that this forum doesn't like smart quotes! Please disregard all the unusual question marks in my post above. Most of them should be changed to an apostrophe.

Also, I'm still interested to hear if anyone has an opinion about the 'cloud' issue of online synced databases with regards to data security risks and confidentiality.

Now I'll get back to distracting myself from writing by exploring Mendeley, Zoot, and Zotero...

Mendeley apparently offers PDF annotation (attaching notes directly to a text passage rather than the entire document). Does anyone know if this feature available in any other application?

A 24-hour update.

I've spent a few hours now reviewing Evernote, Mendeley and Zortero. (There is another review of these three programs here: http://nickprojects.com/category/management/ Here are my quick reflections.

Evernote Pros & Cons
If the number of YouTube videos on how people use it in their everyday is an indication, Evernote seems to be gaining a kind of pop status, primarily among college students. Trendy or not, I found it's online ocr capabilities unmatched in the other programs. Although I haven' t tried it myself, there is a feature for sending images from a mobile phone and getting them automatically uploaded to your database for ocr processing (e.g business cards, menus, street signs) with very little effort. This has very interesting implications for any visual data gathering in the field. I also like the ease with which it handles note-taking and importing multiple file types (limited in the free version). It seems to offer a glimpse of how an internet of things might emerge (but now I'm getting off topic). On the downside, after only a brief amount of testing, my 'Current Monthly Usage' is about half empty which makes the 'Premium' option ($5/mo) a necessity. Also, it doesn't handle pdf markup and you have to log on each time which makes offline work impossible.

Mendeley Pros and Cons
Mendely caters more to the professional academic which I like. However, like Zotero, it's really a citation/reference manager (e.g. Endnote) on crack and not intended for writing text. This was not immediately obvious to me however but perhaps should have been. Still, it's ability to annotate pdfs sets it apart from the others. It also has collaborative features which some people might find useful. Like the other two it can grab and import web selections as individual posts. The most frustrating aspect about Mendeley is the inability to create any kind of arbitrary note on the fly which definitely disqualifies it as a piece of writing software. It only manages imported material.

Zotero Pros and Cons
I don't think I really have much anything new to say about Zotero since it seems like a fairly well known add-on for Mozilla. It's an open source app that feels solid with a strong community of followers. Like Mendeley, it's really a reference manager with some added features over a program like Endnote or Reference Manager. For one, it can search and find the reference information for a given website or pdf which helps reduce data entry. It also permits note-taking. It has a clean interface and I generally like it as well as Mendeley. On the downside, while it does annotate web captures, it cannot markup pdfs which was a disappointment. Also it's tied to Mozilla which means if you're on the net for research you'll probably stuck with Firefox.

In the meantime I found this post that suggests Adobe Bridge can be used for pdf management which was an new twist:
http://peregrina.wordpress.com/2009/01/29/using-adobe-bridge-to-organize-documents/ I'm looking forward to try that out.

Zoot was a disappointment because is only imports the text and looses the pdf layout along with any comments. And similar to most of the other programs recommended in this thread the interface environment is just a little to harsh to be staring at it for more than a few minutes at a time. Maybe it's time to get a Mac after all.

So, I'm still on the look out for the optimal PC Scrivener alternative and may just have to settle for the outline view in Word in the interim. :(

I hope somebody with find this useful!

Cheers, Peter

Peter wrote:

Mendeley apparently offers PDF annotation (attaching notes directly to a text
passage rather than the entire document). Does anyone know if this feature available
in any other application?

Hi Peter,

For PDF annotation I use PDF-XChange Viewer, which I'm very happy with. The website is:

www.docu-track.com

The free version is adequate, but puts a watermark on your PDFs when you use certain advanced features. I eventually paid the very reasonable price ($34.50) for the Pro version, but many people use the free version and are satisfied with it (the free version includes annotation). One feature I particularly appreciate is that you can easily see a summary of all the notes you've taken on a particular document. (The notes show up in the particular passage where you placed them, but they also show up in the convenient summary.) I haven't experimented with Mendeley, so I don't know whether they offer this feature. In general, I find PDF-XChange Viewer to be a very solid and well-designed program.

I store all my PDFs in Zotero, and open them with PDF-XChange Viewer, so that the annotations are immediately saved and backed up. Also, if I open up Zotero on my Mac, the PDF annotations will be visible there too. (And if I want to annotate on the Mac, I just use Preview.)

I confess that Mendeley does sound promising as an integrated solution, but Zotero is currently working well for me, so I don't particularly want to spend the time right now to switch over.

Lucas

Peter,

About Evernote, you wrote:

you have to log on each time which makes offline work impossible

I think you only need to log in if you are going to sync up to the cloud. I had the app save my credentials upon first install of the app on a system, so I am logged in automatically. I create and update notes while offline on a regular basis; they always update via auto sync the next time I'm online. This is true for all three platforms I use regularly: PC, Mac, and iPhone. For iPhone, a note must be marked a favorite for it to be available offline.

Btw, I believe you can create local notebooks that are never sync'd.

Regards,
Wes

Wes Perdue wrote:

Btw, I believe you can create local
notebooks that are never sync'd.

Yes you can. I have a 'temporary' notebook that I have selected not to sync. However, once you choose what type of notebook you want (local or synced) you can't change your mind. This is not as bad as it sounds, because it's very easy to create another notebook of the type you want, select and drag'n'drop all your notes there.

I very often work offline with no problem; all info, including attachments, is available locally. When I'm online again my changes will be synces. I have found no other that does this as seamlessly as Evernote though, as I've written elsewhere (in the post that Peter found me screaming :-), I expect many more information managers to become web-aware eventually.

However, there's one very important reason that Evernote is, for me, completely unsuitable as a writing environment. You'll have a hard time believing it, until you've tried it yourselves: there is no way to create a copy of a note within Evernote --other than create an empty note and copy/paste the content and title- which I find an unacceptable limitation (I have told the developers so, stressing that I am a Premium user, but so far nothing has changed).

So, to put it simply, if you want to use some collected material while preserving the original source, you have to start copying and pasting as if you were in Word.

I know I am late to the party, but as someone who has no only written Ph.D. thesis, but also directed quite a few, I have been wondering about the following:

"Meanwhile, ConnectedText's Win98-like interface, like so much of the PC stuff, doesn't really cut it aesthetically."

What does aesthetics have to do with researching and writing? When I wrote my dissertation I really wanted an IBM Selectric, but not because it was available in different (attractive) colors, but because its correction system was better than anything else available.

In the same way, I suppose that function should dictate form in software tools. As someone who actually uses ConnectedText in his research, I also feel that I need to pint out that its interface is very Win98-like to begin with. (Nor does it need DOSBox to run circles around GrandView --- sorry, but I could not help myself.)

Manfred

Thanks for posting and no worries about coming late to the party.

Point taking about aesthetics and research. I'm no fan of Vista (an example of aesthetic design gone bad). I've stuck with XP. Nevertheless, I suppose I've become accustomed to an increasing degree of let's say 'aesthetic sensibility' in interface design, even for the Windows platform, over that last decade. Something like Evernote may not be your cup of tea, or even mine for that matter (I've decided it's a little too gimmicky for my purposes). Still, if I have the choice, I'll choose a piece of software over another if I think the interface aesthetics is better (cleaner, more intuitive, easy to look at, attractive) provided that the functionality is equal.

Meanwhile, I think I've found my PIM answer for pdf markup and note management: Atlas.ti (http://www.atlasti.com/ It's not cheep but it was sitting under my nose all the time. I already had a copy sitting on my machine for coding and sorting interview transcriptions. The latest version can even import PDFs as well as a range of other media. It might be overkill for some though. Other competitors in the CAQDAS (Computer Aided Qualitative Data Analysis Software) family are Nudist and NVivo.

Still, the actual paper writing process is not facilitated very well (although you can export memo notes into one doc). Hence the search for a Scrivener-like app continues....

...did I read that price correctly? ...woah. And people say The Brain and Notemap are pricey...

Peter wrote:

Thanks for posting and no worries about coming late to the party.

Point taking about
aesthetics and research. I'm no fan of Vista (an example of aesthetic design gone
bad). I've stuck with XP. Nevertheless, I suppose I've become accustomed to an
increasing degree of let's say 'aesthetic sensibility' in interface design, even
for the Windows platform, over that last decade. Something like Evernote may not be
your cup of tea, or even mine for that matter (I've decided it's a little too gimmicky
for my purposes). Still, if I have the choice, I'll choose a piece of software over
another if I think the interface aesthetics is better (cleaner, more intuitive, easy
to look at, attractive) provided that the functionality is equal.

Meanwhile, I
think I've found my PIM answer for pdf markup and note management: Atlas.ti
(http://www.atlasti.com/ It's not cheep but it was sitting under my nose all the
time. I already had a copy sitting on my machine for coding and sorting interview
transcriptions. The latest version can even import PDFs as well as a range of other
media. It might be overkill for some though. Other competitors in the CAQDAS
(Computer Aided Qualitative Data Analysis Software) family are Nudist and
NVivo.

Still, the actual paper writing process is not facilitated very well
(although you can export memo notes into one doc). Hence the search for a
Scrivener-like app continues....

shatteredmindofbob wrote:

...did I read that price correctly? ...woah. And people say The Brain and Notemap are
pricey...

Yeah, but check out the student license --less than 10% of the price.

more info here: http://en.wikipedia.org/wiki/Computer_Assisted_Qualitative_Data_Analysis_Software

The Ethnograph is priced at $99 for students, but I've not used it myself.

Hi again Peter,

Yes, I've heard good things about ATLAS.ti -- clearly useful for processing field notes and the like.

Since I don't think it's been mentioned yet in this thread, I'll just mention one other soon-to-be-available solution, Citavi:

http://www.citavi.com/en/index.html

I think they've been promising an English version for years now, but I trust that it will come out eventually (and they seem to imply that it will be quite soon).

@Manfred--

You convinced me to give CT another shot!

Lucas

Hi Lucas,

Thank you for all the tips! It seems to me like you have a developed a great research workflow integrated with some cool apps. Do you mind summarizing it here for us (well at least for me) i.e. an overview of your entire process from data collection to analysis and writing and how the software fits in? You've already mentioned a few applications that you like (Zotero, PDF-XChange Viewer) but I am curious to get an overview of how you fit all the pieces altogether. ;)

If this is too much trouble then no worries. I just thought I'd ask. I'll try to sketch mine to give you an idea of what I mean.

Literature search:
I use some of the more traditional tools like Web of Science but have come to love Google Scholar. It integrates a bib manager link that can be used to import the source directly into the database (e.g. Endnote or BibTex).

Qualitative data analysis:
Up to now I've used ATLAS.ti. It's a comprehensive program for coding a range of media including txt, doc, pdf, audio and video. However, I'm finding it slow when it comes to searching pdfs. Still, it's one of the few programs that allows annotation and searching of pdf files as well as text docs like interview transcripts. In the future I might use it to replace Endnote but currently it does not have a bibliographic mode. I'm also looking forward to try out PDF-XChange Viewer. :)

Citation management:
I've been using Endnote for many years. I have a library of over 1000 pdfs. On nice feature its ability to 'package' the entire database and move or back it up to a different computer. One problem however is that it doesn't allow full-text searches of the pdf content. For this reason I've been cutting and pasting the abstract into the abstract field to permits searching for relevant keywords. I can also add my reading notes to the same post. It easily imports the reference into Word as you write and creates a fully formatted bibliography at the end of the paper. Some interesting bibliographic alternatives are Mendeley and Zotero.

Brainstorming and mind-mapping:
Freemind is a great like open source program that I love.

Drafting and writing
Word has been my main tool. I make us of the outline function especially for long reports. However, like many out there I have the problem of creating new drafts every week or so and end up with loads of file versions scattered across multiple folders. Scrivener seems like a solution to this problem. Hence my interest in this forum!

Best,

Peter

Hi Peter,

Sorry for the delayed response. My academic workflow is far less worked out than you might have guessed---i'm still trying to come up with a workable system. In fact, I decided finally to take the ConnectedText plunge recently, so all of a sudden my "workflow" has totally changed. So far so good, although it's too soon to conclude whether I'll stick with CT. Once my system is better worked out---or, more to the point, once my system has shown results in terms of my academic work---i'll share in more detail the elements of the system.

Best,
Lucas

Great! I look forward to reading all about it when you get the chance.:)

In the meantime does anyone have recent experience to share with pdf annotation / markup?

Lucas wrote:

Hi Peter,

Sorry for the delayed response. My academic workflow is far less worked
out than you might have guessed---i'm still trying to come up with a workable system.
In fact, I decided finally to take the ConnectedText plunge recently, so all of a
sudden my "workflow" has totally changed. So far so good, although it's too soon to
conclude whether I'll stick with CT. Once my system is better worked out---or, more to
the point, once my system has shown results in terms of my academic work---i'll share
in more detail the elements of the system.

Best,
Lucas

Manfred wrote:

I know I am late to the party, but as someone who has no only written Ph.D. thesis, but
also directed quite a few, I have been wondering about the following:

"Meanwhile,
ConnectedText's Win98-like interface, like so much of the PC stuff, doesn't really
cut it aesthetically."

What does aesthetics have to do with researching and
writing? When I wrote my dissertation I really wanted an IBM Selectric, but not
because it was available in different (attractive) colors, but because its
correction system was better than anything else available.

But what if the Selectric was lacking in subjective appeal for some reason _relevant_ to its _function_; say, you couldn't stand the way the keys felt, even though you could type fast and accurately enough? That would seem a better analogy for the aesthetics of an interface; just as a typewriter keyboard is for typing, an application's interface is for?looking.

In the same way, I
suppose that function should dictate form in software tools. As someone who actually
uses ConnectedText in his research, I also feel that I need to pint out that its
interface is very Win98-like to begin with. (Nor does it need DOSBox to run circles
around GrandView --- sorry, but I could not help myself.)

Manfred