OT: What reference management software do you use?

OT: What reference management software do you use?

[Paul Menzel]

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Dear ConTeXt folks,


using ConTeXt and not LaTeX you maybe also use a nice reference
management software the main stream does not know about. But probably it
is not related to ConTeXt at all since it is BibTeX in the end.

I found a comparison in Wikipedia [1] and consider to use JabRef.


Thanks,

Paul


[1] https://secure.wikimedia.org/wikipedia/en/wiki/Comparison_of_reference_management_software

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Re: OT: What reference management software do you use?

[Joerg.Hagmann]

Hi Paul,

I recently switched from "Papers" (Mac only, commercial) to JabRef.  
Advantages: JabRef is open source, and I can use it at work (Macs) and  
at home (Linux). I like it -- it has everything I need (searching  
PubMed etc., managing a collection of pdf-files...).

Cheers, Jörg

Quoting Paul Menzel <paulepanter@users.sourceforge.net>:

> Dear ConTeXt folks,
>
>
> using ConTeXt and not LaTeX you maybe also use a nice reference
> management software the main stream does not know about. But probably it
> is not related to ConTeXt at all since it is BibTeX in the end.
>
> I found a comparison in Wikipedia [1] and consider to use JabRef.
>
>
> Thanks,
>
> Paul
>
>
> [1]  
> https://secure.wikimedia.org/wikipedia/en/wiki/Comparison_of_reference_management_software
>



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Re: OT: What reference management software do you use?

[Otso Helenius]

>using ConTeXt and not LaTeX you maybe also use a nice reference
>management software the main stream does not know about. But probably it
>is not related to ConTeXt at all since it is BibTeX in the end.

I can warmly recommend Zotero. It works very well and can fetch content
directly from web pages (also recognizes PubMed, ScienceDirect, Google Books
etc. automatically). The best feature is automatic sync of content
to either the Zotero server or your own.

The Firefox plugin is nice, and now there is also an alpha standalone app
in in development. The software is open source and in use in many
universities worldwide.

http://www.zotero.org/about/

Best,
Otso Helenius
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Re: OT: What reference management software do you use?

[Pontus Lurcock]

On Sat 21 May 2011, Paul Menzel wrote:

> using ConTeXt and not LaTeX you maybe also use a nice reference
> management software the main stream does not know about. But
> probably it is not related to ConTeXt at all since it is BibTeX in
> the end.

As someone using stone-age reference management (i.e. a plain BibTeX
file maintained by hand), I found the emacs snippet at the bottom of
http://www.emacswiki.org/emacs/RefTeX incredibly useful. If you have
the cursor over a bibliography key, it lets you open the corresponding
pdf (or ps, dvi, djvu etc.) with a single keystroke.

I've tried JabRef, Referencer, Mendeley and various others but plain
emacs (I don't use RefTeX) and that snippet still seem to work best
for me.

Pont
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Re: OT: What reference management software do you use?

[Stefan Müller]

On 22.05.2011 22:14, Otso Helenius wrote:
>> using ConTeXt and not LaTeX you maybe also use a nice reference
>> management software the main stream does not know about. But probably it
>> is not related to ConTeXt at all since it is BibTeX in the end.
>
> I can warmly recommend Zotero. It works very well and can fetch content
> directly from web pages (also recognizes PubMed, ScienceDirect, Google Books
> etc. automatically). The best feature is automatic sync of content
> to either the Zotero server or your own.

+1 for Zotero

I tried Mendeley some time ago. It's standalone but sill quite similar 
to Zotero. "Browser-integration" works via a special bookmark. It also 
has an embedded pdf-viewer, which is very neat. Reason for changing to 
Zotereo were some strange bibtex-export issues, where the bibtex file 
got messed up and had to be readjusted manually.

> The Firefox plugin is nice, and now there is also an alpha standalone app
> in in development. The software is open source and in use in many
> universities worldwide.
>
> http://www.zotero.org/about/
>
> Best,
> Otso Helenius
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Re: OT: What reference management software do you use?

[Thomas A. Schmitz]

On May 23, 2011, at 10:45 PM, Stefan Müller wrote:

> +1 for Zotero
> 
> I tried Mendeley some time ago. It's standalone but sill quite similar to Zotero. "Browser-integration" works via a special bookmark. It also has an embedded pdf-viewer, which is very neat. Reason for changing to Zotereo were some strange bibtex-export issues, where the bibtex file got messed up and had to be readjusted manually.

I find Zotero useless for my work with ConTeXt. You cannot have cross-references within your bibliographic items, and it is impossible to have proper markup in bibliographical items. For me, both are absolute killer arguments; I cannot work with zotero. And the bibtex export sucks; important features such as bibtex strings are not supported. So I would actually recommend jabref if you need a cross-platform tool or bibdesk if you're using OS X exclusively. Regarding a system when you write your context files: I use Emacs, and I haven't seen anything more powerful or more convenient than reftex (which also works with context, after a few tweaks in your configuration file).

Thomas
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Re: OT: What reference management software do you use?

[Stefan Müller]

Okay, then I should definitely take a look at JabRef. Anyhow, maybe I'm 
naive here, but I don't see a reason why Zotero should support BibTeX 
Strings. If I type the BibTeX file manually, sure. But Zotero reads the 
(e.g.) Journal names from the corresponding websites, so there should be 
no need to replace those with abbreviations. Is it because I don't 
understand BibTeX strings?

Does JabRef offers synchronisation (e.g. WebDAV) between different machines?

Stefan

On 23.05.2011 23:00, Thomas A. Schmitz wrote:
>
> On May 23, 2011, at 10:45 PM, Stefan Müller wrote:
>
>> +1 for Zotero
>>
>> I tried Mendeley some time ago. It's standalone but sill quite similar to Zotero. "Browser-integration" works via a special bookmark. It also has an embedded pdf-viewer, which is very neat. Reason for changing to Zotereo were some strange bibtex-export issues, where the bibtex file got messed up and had to be readjusted manually.
>
> I find Zotero useless for my work with ConTeXt. You cannot have cross-references within your bibliographic items, and it is impossible to have proper markup in bibliographical items. For me, both are absolute killer arguments; I cannot work with zotero. And the bibtex export sucks; important features such as bibtex strings are not supported. So I would actually recommend jabref if you need a cross-platform tool or bibdesk if you're using OS X exclusively. Regarding a system when you write your context files: I use Emacs, and I haven't seen anything more powerful or more convenient than reftex (which also works with context, after a few tweaks in your configuration file).
>
> Thomas
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Re: OT: What reference management software do you use?

[John Haltiwanger]

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I hope my question does not come off as too aggressive, but why on earth are
we still using BibTeX? Or, more accurately, when can we _stop_ using BibTeX
and move onto something that has native UTF-8 support and can also integrate
with a reasonable configuration environment such as CSL?

What is the next step for bibliographies in Context? Surely we won't be
chained to BibTeX (which has seemingly been largely been in practice for the
sake of BibLaTeX) forever?

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Re: OT: What reference management software do you use?

[Pontus Lurcock]

On Mon 23 May 2011, Stefan Müller wrote:

> Okay, then I should definitely take a look at JabRef. Anyhow, maybe I'm  
> naive here, but I don't see a reason why Zotero should support BibTeX  
> Strings. If I type the BibTeX file manually, sure. But Zotero reads the  
> (e.g.) Journal names from the corresponding websites, so there should be  
> no need to replace those with abbreviations. Is it because I don't  
> understand BibTeX strings?

I believe that one advantage is adding a level of indirection for
journal naming: you can have, for example, one definition file which
defines JISN as ‘Journal of Inconveniently Sesquepedalian
Nomenclature’, and another defining it as ‘J. Inc. Ses. Nom.’, and
switch between different definition files according to publisher
requirements, space restrictions, and so on.

Pont
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Re: OT: What reference management software do you use?

[Otso Helenius]

> What is the next step for bibliographies in Context? Surely we won't be
> chained to BibTeX (which has seemingly been largely been in practice for the
> sake of BibLaTeX) forever?

Perhaps Biber (http://biblatex-biber.sourceforge.net/) could fill the void.
It supports Unicode, is BibTeX compatible and has planned SQL and XML support
in the future.

I'm happy as long as the next de facto scientific standard for references will
be open source and not something as horrible as RefWorks.

Best,
Otso Helenius
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Re: OT: What reference management software do you use?

[Thomas A. Schmitz]

On May 23, 2011, at 11:32 PM, John Haltiwanger wrote:

> I hope my question does not come off as too aggressive, but why on earth are we still using BibTeX? Or, more accurately, when can we _stop_ using BibTeX and move onto something that has native UTF-8 support and can also integrate with a reasonable configuration environment such as CSL?
> 
> What is the next step for bibliographies in Context? Surely we won't be chained to BibTeX (which has seemingly been largely been in practice for the sake of BibLaTeX) forever?

You do sound a bit impatient, but the answer is: bibtex is a beast, but bibliographies is such an endless topic, there are so many permutations and possibilities and options that "replacing bibtex" is easier said than done. bibtex gets the job done, most of the time, and I've always heard that there will be a "next big thing which will replace bibtex," but it never quite happened. zotero's approach (a completely untransparent, complex and hence fragile sql database) is a lot worse than bibtex. 

As to the question "why strings": Pontus's answer named one important aspect. I have several .bib files which contain nothing but string definitions: one with abbreviated, one with full journal titles; one with English strings ("reprint," "Munich") and one with the German equivalent ("Nachdruck," "München"). Including the right file(s) will then provide the desired output.

Thomas
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Re: OT: What reference management software do you use?

[Stefan Müller]

On 23.05.2011 23:47, Thomas A. Schmitz wrote:
> As to the question "why strings": Pontus's answer named one important aspect. I have several .bib files which contain nothing but string definitions: one with abbreviated, one with full journal titles; one with English strings ("reprint," "Munich") and one with the German equivalent ("Nachdruck," "München"). Including the right file(s) will then provide the desired output.

That sounds quite reasonable. I haven't thought of that yet, as I 
haven't written a lot of bibliographies and they were all in English.

If I have for example mybib.bib, en.bib and de.bib, how would I tell 
ConTeXt that it should use mybib.bib as database and en.bib for string 
replacement?
   \setupbibtex[database={mybib.bib,en.bib}]
?

Stefan
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