Very intriguing research application (free and multiplatform)

[Eric Durbrow]

If you are interested in seeing if the web can help with your research
and writing you might try this...

http://www.mendeley.com/how-it-works/

Basically, you upload your publications or writings and Mendeley
extracts papers and sets up a list allow sharing and biblio research.
It is free and runs on Windows, Mac OS X, and Linux. Please let me
know what you think!

Disclaimer: I have NO connection to the company.

E. Durbrow Ph.D. dur...@gmail.com 90202
Profile: http://www.google.com/profiles/Durbrow
Voicemail! (818) 584-1137
Teaching: http://homepage.mac.com/durbrow/Courses/
Reading: http://psycmeetsreality.tumblr.com/ or
http://www.google.com/reader/shared/16296206292021843372
or http://friendfeed.com/durbrow or twitter: durbrow
Helping: www.ripple.org or www.thehungersite.com

[Mark Andersen]

One of my graduate students uses Mendeley and really likes it. I can see where it would be useful for a group of collaborators to share references/readings. I've recently switched from EndNote to Zotero; it seems that both of those programs have a somewhat different purpose than programs/services like Mendeley and Connotea. I'd like to see some concrete examples of the use of Mendeley in research (and in teaching?).

Mark Andersen

Department of Fish Wildlife and Conservation Ecology

New Mexico State University

--
Dr. Mark C. Andersen
Las Cruces, NM

[Ru]

Another similar application I came across recently was scholarz.net;
they add the capability of outlining and linking your references to
notes and outlines as you work. What interested me about scholarz is
that it was started and run by a group of phd students in non-computer
disciplines who were looking for a solution to their own research
challenges.

I do wonder, however, how these tools will fare once Zotero can truly,
easily and seemlessly share reference libraries across multiple
computers and accounts. At that point the collaborative reference
management piece of these tools will be less unusual and the other
features will come to the forefront.

Rebecca
protos...@gmail.com
http://protoscholar.com

On Jun 21, 6:18 am, Mark Andersen <drmarkander...@gmail.com> wrote:
> One of my graduate students uses Mendeley and really likes it. I can see
> where it would be useful for a group of collaborators to share
> references/readings. I've recently switched from EndNote to Zotero; it seems
> that both of those programs have a somewhat different purpose than
> programs/services like Mendeley and Connotea. I'd like to see some concrete
> examples of the use of Mendeley in research (and in teaching?).
> Mark Andersen
> Department of Fish Wildlife and Conservation Ecology
> New Mexico State University
>
>
>
> On Sat, Jun 20, 2009 at 10:47 AM, Eric Durbrow <durb...@gmail.com> wrote:
>
> > If you are interested in seeing if the web can help with your research
> > and writing you might try this...
>
> >http://www.mendeley.com/how-it-works/
>
> > Basically, you upload your publications or writings and Mendeley
> > extracts papers and sets up a list allow sharing and biblio research.
> > It is free and runs on Windows, Mac OS X, and Linux. Please let me
> > know what you think!
>
> > Disclaimer: I have NO connection to the company.
>

> > E. Durbrow Ph.D. durb...@gmail.com 90202

[aarondesk]

I'm very interested in this software. Not necessarily for making
bibliographies or the online sharing features (though this could be
nice), but mostly as a way to organize pdf files. I've always wanted a
program to organize and tag pdf files, but I don't know of a good
solution for Windows. I know such software exists very nicely for
Macs, but Mendeley my fit the bill for Windows machines.
Aaron

[CB]

On Jun 21, 2:47 am, Eric Durbrow <durb...@gmail.com> wrote:
> If you are interested in seeing if the web can help with your research  
> and writing you might try this...
>
> http://www.mendeley.com/how-it-works/
>
> Basically, you upload your publications or writings and Mendeley  
> extracts papers and sets up a list allow sharing and biblio research.  
> It is free and runs on Windows, Mac OS X, and Linux. Please let me  
> know what you think!

Mendeley's coming on pretty fast, but the desktop application is still
quite crude compared to the established alternatives like Zotero. It
doesn't have nested collections, and the metadata extraction is less
than perfect. Also somewhat critically for academic work, imo:
Mendeley lacks support for non-pdf sources (full-text html) and for
ezproxy (zotero's support for both is great).

The web application, on the other hand, is well ahead of the
'competition'. The developers are also remarkably responsive, and via
their forums are making a real effort to solicit user input. It also
looks like they have quite a bit of funding, which you'd want to be
confident enough to commit time/data to their system.

I have it installed, but use Zotero for day-to-day stuff. Mendeley is
'one to watch'.

[aarondesk]

I never got too excited about Zotero. Maybe I'm not web 2.0 compliant,
but having a program run as a web browser extension just doesn't sit
well with me.

My impression is that Zotero and Mendeley have different (but not
exclusive) target audiences. I'm guessing 95+% of those in science and
engineering work almost entirely with pdf files (journal articles),
whereas this may not be the case for the humanities, social sciences,
etc.

Just my 2 cents.
Aaron

[CB]

On Jun 27, 12:20 am, aarondesk <aarond...@gmail.com> wrote:
> I never got too excited about Zotero. Maybe I'm not web 2.0 compliant,
> but having a program run as a web browser extension just doesn't sit
> well with me.

This seems a rather unsubstantial point. Firefox/XUL provided the
zotero devs with a nice, mature, full-featured app framework, and
natural ways to integrate with online scholarly databases. Some of the
things zotero can offer as a result (eg. the url-rewriter support)
are really unparalleled by any other software. I don't see that it
being implemented as an extension has any concrete disadvantages.

> My impression is that Zotero and Mendeley have different (but not
> exclusive) target audiences. I'm guessing 95+% of those in science and
> engineering work almost entirely with pdf files (journal articles),
> whereas this may not be the case for the humanities, social sciences,
> etc.

True but becoming less so. Open journals are pushing nicely marked-up
html versions. PDFs are still dominant, as you say especially in the
sciences, but I think the trend is away from them.

One nice thinb about Mendeley is that its devs seem not to suffer from
an either/or competitive mentality. They've already partly implemented
CiteULike integration, and they've expressed willingness to work with
Zotero. That must be good.

[Jan Erik Moström]

On 09-06-26 at 08.08, CB <cb.l...@gmail.com> wrote:

>This seems a rather unsubstantial point. Firefox/XUL provided the
>zotero devs with a nice, mature, full-featured app framework, and
>natural ways to integrate with online scholarly databases. Some of the
>things zotero can offer as a result (eg. the url-rewriter support)
>are really unparalleled by any other software. I don't see that it
>being implemented as an extension has any concrete disadvantages.

Personally I think is a nice idea but I would like to see a
stand-alone application with a much improved user interface -
it's the user interface that is the main reason why I don't use
Zotero, the dependency on FF the second.

jem
--
Jan Erik Moström, http://mostrom.eu

[CB]

On Jun 27, 5:02 pm, Jan Erik Moström <most...@gmail.com> wrote:
>
> Personally I think is a nice idea but I would like to see a
> stand-alone application with a much improved user interface -
> it's the user interface that is the main reason why I don't use
> Zotero, the dependency on FF the second.
>

Out of interest, what do you use? I haven't found anything with a
really good UI yet. Endnote's a horror ...

[Doctor alf]

Whilst it's Mac OS only, Mekentosj's Papers has an excellent interface. It is essentially the same as Mendeley, except that it works now without the bugs or instability.

I disagree that PDF is on the way out and HTML is on the way in. HTML will never look as good printed as PDF does. I find the need for a reference manager that can handle supplementary materials, corrigendi and such more important than one that handles HTML well. But that's just my bias.

d

--
"... better to be Socrates dissatisfied than a fool satisfied."

[Jan Erik Moström]

> Out of interest, what do you use? I haven't found anything with a
> really good UI yet. Endnote's a horror ...

I heven't found anything really good but the app that has given me the
least problems is Bookends. Gave up on Endnote some 10 years ago,
jabref also had some UI issues, BibDesk - I had some problems with it.
And some of the others didn't support bibtex.
--
Jan Erik Moström, mos...@gmail.com

[arehrlich]

If you are looking for a good application to organize pdf's you might
want to look at Benubird. The website talks about a Pro version that
is not ready yet, but on their download page they say that the
application is now free.

http://www.debenu.com/benubird/trial.html

I've been using it for a few months and find it easy to use and very
powerful.

Alan

[CB]

On Jun 28, 12:02 pm, Doctor alf <doctor....@gmail.com> wrote:
> Whilst it's Mac OS only, Mekentosj's Papers

> <http://mekentosj.com/papers/>has an excellent interface. It is

> essentially the same as Mendeley, except
> that it works now without the bugs or instability.

I'll consider a Mac when they make a tablet ..

> I disagree that PDF is on the way out and HTML is on the way in. HTML will
> never look as good printed as PDF does. I find the need for a reference
> manager that can handle supplementary materials, corrigendi and such more
> important than one that handles HTML well. But that's just my bias.
>

My main point was really just that PDF-storage alone (Mendeley) isn't
enough. For academic research/citation software it doesn't even make
sense, since PDF is just one format amongst others. There's no logic
behind coralling them off into a separate organisational app.

Zotero does a good job of keeping heterogenous bits and pieces
together.

[CB]

On Jun 29, 7:55 am, arehrlich <arehrl...@gmail.com> wrote:
> If you are looking for a good application to organize pdf's you might
> want to look at Benubird.  The website talks about a Pro version that
> is not ready yet, but on their download page they say that the
> application is now free.
>
> http://www.debenu.com/benubird/trial.html
>

Thanks for the tip -- from the website it looks like it's PDF-only.

[Jeanne Edna Thelwell]

Actually, the website says that it's "Optimized for use with PDFs, images, and Microsoft Office and OpenOffice documents".  I'm downloading it now.

--
Jeanne
------------------
"Technique without ideals is a menace.  Ideals without technique are a mess." -- Karl Llewellyn

[CB]

On Jun 21, 2:47 am, Eric Durbrow <durb...@gmail.com> wrote:

> If you are interested in seeing if the web can help with your research  
> and writing you might try this...
>
> http://www.mendeley.com/how-it-works/
>

Mendeley have just released a new client -- includes PDF annotation,
along with some other nice new stuff.

[anatolica]

On Jul 7, 3:12 am, CB <cb.li...@gmail.com> wrote:

> Mendeley have just released a new client -- includes PDF annotation,
> along with some other nice new stuff.

I have been tinkering with Mendeley ever since they were beta 0.4 or .
5, and this latest version seems really a big improvement. this PDF
viewing-annotation feature with a nice interface is a real plus
think. I tested in Ubuntu and windows xp; some features (search) seems
disabled for now but overall it is a promising beta for a good
software, and I find them responsive to user requests -see their user
feedback sites. There you can see that there are a lot of requests for
some sort of integration with Zotero, and the company seems to follow
a rather collaborative approach towards such ideas.

Ever fond of open source software, I depend on (and adore) Zotero, and
I find Zotero and Mendeley complementary to each other -which I
believe is something that will develop even further in the future.
Commercial product wise, I appreciate fair players and I think
Mendeley seems one of them. I like both.

[rickdude]

So far, I've tended to use CiteULike to gather references. I like it
because of its extensive set of plugins, the flexible Lucene search,
and ways to view your library or others' libraries through tags (or
even tag fragments). CuL has never struck me as being the best way to
organize my own notes on sources, though. For that, I use Bookends,
because it's priced quite low, the developer is very responsive, and,
as Jan said earlier, it gives very few problems. It also is pretty
good at importing CuL data.

I've never really liked the Zotero interface, though I agree that the
new collaboration features make it more attractive than before. I had
never heard of Mendeley until I saw this thread, but I'm very
impressed: I think having a web app and a desktop app is a great idea,
and the collaboration features are well thought-out.

However, it seems to me that there's nothing to beat Sente (Mac only)
on the workflow front. It has ultra-flexible collections and sub-
collections. The killer is the notetaking features; they have a video
(about 2 minutes) demonstrating how it works:
http://www.thirdstreetsoftware.com/site/videos/notes.html

Scholarz.net looks a bit raw at the moment, but is a fascinating idea.
This is a pretty exciting time in the reference management field.

[rickdude]

What is ezproxy?

[CB]

On Aug 11, 10:44 pm, rickdude <rickla.r...@gmail.com> wrote:
> What is ezproxy?
>

It is the most common (I think) way for universities to provide off-
campus access to subscribed online journals. It's not a true proxy,
but rather a url-rewriter that allows requests to go via your
institution, eg a url like http://www.sciencedirect.com/blah might
become http://www.sciencedirect.com.ezproxy.youruni.edu.au/blah.

Zotero has a really nice feature to assist here: once it's detected
that you go to a certain site via a proxy, it can automatically add
that proxy suffix to your urls when you browse there, making access to
paid sites very easy.