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mattmarshall · Oct 4, 2006, 05:00 AM

Hey Guys

I'm looking for software, that may nor may not exist.

I have a lot of PDF's and Html files of articles and recipes. Books. All sorts of stuff, that I keep in a Bookshelf folder in my Home folder.

Browsing isn't so great. What I need is a sort of iTunes for documents. Digital Library I can browse through, sort into folders of related stuff, whatever.

Does this exist?

Matthew Marshall

philm · Oct 4, 2006, 06:49 AM

Yojimbo?

slugslugslug · Oct 4, 2006, 09:28 AM

I remember thinking Yep looked pretty cool, back when it was called Kip, but I haven't seen a lot of details about it. But they bill it as iPhoto for PDFs.

OTOH, it may not deal with HTML..

CatOne · Oct 4, 2006, 02:04 PM

IMO DEVONthink is about the best for this:

DEVONthink

Yojimbo is also a good option. It is faster for text notes, but its category system is a bit less flexible. I also have concerns about throwing as many PDFs in it as you can in DEVONthink. My DT database is about 1.6 GB now.

infowarrior · Oct 5, 2006, 01:11 AM

I use Bookends for my PhD document management -- great to keep references organized and also have the original document(s) handy. Was I think $99 but IMO it's well-worth it. Very user-friendly and powerful.

There's also Thompson EndNote, but not many of my fellow doctoral candidates really like it. They use it, but hate it.

OreoCookie · Oct 5, 2006, 03:39 AM

iView Media Pro can read pdfs (only on the Mac version) and docs that.

workerbee · Oct 5, 2006, 03:50 AM

Originally Posted by CatOne

My DT database is about 1.6 GB now.

My DT has become quite slow recently - when I sent it a link from OmniWeb through the Service menu, it takes so long to start that the link gets forgotten somewhere along the way. My DT database is only 426 MB... I hate to think what would happen if it was 1.6GB...

TheIceMan · Oct 5, 2006, 03:59 AM

I second the vote for Yojimbo. I was a former user of DevonThink Pro but as workerbee mentioned, it started getting slower and slower to launch and manage as the library grew. Right now, I've been on Yojimbo for a few months and I'm pretty happy with it. Like, DevonThink, Yojimbo can handle all sorts of files, such as pdfs, word doc, txt, even quicktime videos AND it's much faster!

Macanoid · Oct 5, 2006, 07:22 AM

Another vote for Devonthink Pro here. It's incredidably versatile and it's got amazing support.

With regards to Yojimbo, I agree it's nice, but at the moment it can match DTP's features. For instance, it doesn't support nested folders yet, which is essential for me.

I suggest you try out both!

CatOne · Oct 5, 2006, 11:26 AM

Originally Posted by workerbee

My DT has become quite slow recently - when I sent it a link from OmniWeb through the Service menu, it takes so long to start that the link gets forgotten somewhere along the way. My DT database is only 426 MB... I hate to think what would happen if it was 1.6GB...

What kind of link? Is it a web archive? Can't imagine that one bad file would slow the whole application down. That said, if you an RTF file with lots of tables in it (maybe the same with HTML files) then displaying that specific file could be slow. Mine is loaded up with PDF files for the most part, and about 8000 RTF documents which are notes from conversations with customers.

You may want to post your issues on their forums... they're very quick and responsive at responding.

kman42 · Oct 5, 2006, 02:49 PM

For serious scientific reference management, Bookends can't be beat. And it keeps getting better with each release.

Just for tracking random bits of information? I haven't found a great solution yet. Of course, by great I mean that it will sync with multiple computers (some do) AND a mobile device (some do). I haven't found any that do both well.

kman

hemant · 03:24 PM

I use EndNote for my reference management, and it really sucks. It has become almost impossible to work with it. The windows version is not bad though.

kman42 · Oct 5, 2006, 05:04 PM

Originally Posted by hemant

I use EndNote for my reference management, and it really sucks. It has become almost impossible to work with it. The windows version is not bad though.

Seriously, give Bookends a try. I switched about 18 months ago and haven't looked back. I'm not sure if they have a demo or anything, but all the upgrades have been free so far, even a major release.

kman

hemant · Oct 5, 2006, 11:19 PM

Originally Posted by kman42

Seriously, give Bookends a try. I switched about 18 months ago and haven't looked back. I'm not sure if they have a demo or anything, but all the upgrades have been free so far, even a major release.

kman

I got a demo version of Bookends and it was able to import my EndNote database without a glitch. I think I want to use it the only issue I see is that I'm pretty close to completing my thesis and I have EndNote citations all over the document. Can Bookends scan my document and start managing my citations?

jasong · Oct 6, 2006, 07:04 AM

If you're really close to finishing, then do yourself a favor a wait until you are done. Do you really want to mess with learning new software and all the risks that come with conversion when the end is in sight? If it's gotten you this far, it's at least bearable. Finish with what you've got, them learn the new software for next time.

slugslugslug · Oct 6, 2006, 08:49 AM

With all due respect to hemant, some people are "really close to finishing" their thesis for a few years on end.

Also, if he/she can afford to buy the software, it couldn't hurt to try it. I mean, you back up your original, import it, and make very few changes until you've determined whether the new software munged your old work and whether you like it better. If it does turn out to be way easier to use, it might be possible to make up the time spent learning it with the time saved by using it, even in the course of a semester.

hemant · Oct 6, 2006, 11:22 AM

Actually I did have to move to Windows (via parallels), to continue working without the delay and hanging issues I have been having lately with EndNote. I was soo happy with LaTeX, but my advisor had trouble correcting my work, so had to switch.

OreoCookie · Oct 6, 2006, 11:26 AM

Originally Posted by hemant

Actually I did have to move to Windows (via parallels), to continue working without the delay and hanging issues I have been having lately with EndNote. I was soo happy with LaTeX, but my advisor had trouble correcting my work, so had to switch.

How can you have trouble correcting LaTeX files? The output is just a neat pdf …

kman42 · Oct 6, 2006, 12:35 PM

I'm not sure if Bookends can replace Endnote citations or not as I never faced that issue. I made a clean break several months before writing my thesis so I was just able to import all of my refs from Endnote and start using Bookends right away. There are some very responsive forums on the Bookends website where you could pose your question and get a prompt reply.

hemant · Oct 6, 2006, 12:38 PM

Originally Posted by OreoCookie

How can you have trouble correcting LaTeX files? The output is just a neat pdf …

You can't edit pdf, can you?

jmgriff · Oct 6, 2006, 12:49 PM

If you are comfortable with LaTeX, thenBibDesk is a nice way to keep your PDFs and references organised. It's free too. Doesn't have the kind of Word integration that Endnote, BookEnds or Sente offer - but I usually use its smart groups feature to keep track of references for a given doc and then use the preview function to render them. I was really unhappy with Endnote and had endless problems with CWYW.

Also check out Journler, as a possible free alternative to YoJimbo or DevonThink.

OreoCookie · 02:20 PM

Originally Posted by hemant

You can't edit pdf, can you?

No, but what's wrong with paper? That's how we do it here …
I don't think we ever edit each others texts directly in the file, even among collaborators.

hemant · Oct 6, 2006, 02:27 PM

But my advisor likes to go over my work and suggest corrections, improvements. I do the same with his work. If both are at the same location (most of the time) then may be a hard copy (of the pdf) would be a good idea. Still don't you think that's double the amout of work. If all the authors of the paper are comfortable using LaTeX then it would be great if not, I prefer Word, turn on the "track changes" option and everything seems good. Not that I'm a big fan of Word but, it gets things done.

As for Bookends, they do have a way to convert EndNote citations. For future reference:

a) Export the bibliography from EndNote as an XML file and then import it in Bookends.
b) Open the document and use the option "unformat citations" from EndNote menu.
c) Now scan the document via Bookends and everything is in place.

I still have to format my citations and bibliography to suit my needs but that shouldn't be a lot of work.

kman42 · Oct 6, 2006, 03:08 PM

Cool that Bookends will work with you Endnote citations.

One VERY nice addition to the latest version of Bookends is that you can select a reference and it will go out and try to find the full-text PDF for you and attach it. Depending on your institution, it works with many of the big journals. I was able to collect pdfs to old refs in over 50% of cases without a problem.

OreoCookie · Oct 6, 2006, 03:39 PM

Originally Posted by hemant

But my advisor likes to go over my work and suggest corrections, improvements. I do the same with his work. If both are at the same location (most of the time) then may be a hard copy (of the pdf) would be a good idea. Still don't you think that's double the amout of work. If all the authors of the paper are comfortable using LaTeX then it would be great if not, I prefer Word, turn on the "track changes" option and everything seems good. Not that I'm a big fan of Word but, it gets things done.

No, because it's just a matter of etiquette where I am (I'm not saying everybody should do it that way). You propose a change by commenting it. Personally, I don't care whether you do it electronically (via Adobe Reader or Preview for instance) or on the paper. Reading comments in LaTeX source code is also not as convenient. We usually now scan our pages with the copy machine and then send everything by e-mail -- which is more convenient anyway since my co-author now has a professorship in Italy.

milhouse · Oct 7, 2006, 11:39 AM

Originally Posted by workerbee

My DT has become quite slow recently - when I sent it a link from OmniWeb through the Service menu, it takes so long to start that the link gets forgotten somewhere along the way. My DT database is only 426 MB... I hate to think what would happen if it was 1.6GB...

Verify and repair the database. If that doesn't work, rebuild it.
You might also perform maintenance on OS X. Many of the issues users have on their forums are related to OS X, not DT or DTPro.

workerbee · Oct 8, 2006, 02:36 PM

Originally Posted by milhouse

Verify and repair the database. If that doesn't work, rebuild it.

Actually, I've found that while opening DT the first time after a reboot (or after updating DT) is quite slow -- so slow that an URL sent over the services menu from OmniWeb to DT tends to get lost somewhere inbetween -- it usually works after that, even if I don't keep DT open all the time.