Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Niels Kobschätzki]

On Jun 22, 2007, at 7:41 PM, Alexander H. Montgomery wrote:

>
> On Jun 22, 2007, at 8:26 AM, Niels Kobschätzki wrote:
>
>> On Jun 22, 2007, at 5:03 PM, Adam R. Maxwell wrote:
>>
>>>
>>> On Jun 21, 2007, at 23:08, Niels Kobschätzki wrote:
>>>
 On Jun 22, 2007, at 7:52 AM, Niels Kobschätzki wrote:
> I just found out that I could use iTunes for managing PDFs. It
> allows
 me to do a fast search on them (Genre: Papers; Artist: Author-Name;
 Title: Paper-name; Comments: Keywords) and they are organized in  
 one
 place (iTunes-Music-library) which gets backed up regularly.
>>>
>>> I'm guessing it doesn't allow you to search by content, though?  It
>>> really depends on what you need.
>>
>> Most of the "interesting" stuff is non-OCR-JSTOR-stuff anyway -- I
>> gave up the illusion to search the content of my pdfs (and stuff in
>> iTunes can be handled by Spotlight). Some kind of tagging and not
>> thinking about the managing in the file-system is more important to
>> me.
>>
>> Niels
>
> All of JSTOR is now OCRed. If you have the permanent URLs in
> BibDesk's URL field, you can use my JSTOR Download PDF script to grab
> the new versions, which are also smaller. (Warning: They are
> compressed with JBIG2, which Apple's PDFKit is slow at rendering)
>
> http://people.reed.edu/~ahm/Projects/Citation/BibDesk/
>
> Note that the script won't work through a proxy, only when you have
> direct campus access.

Thx for the script and the note the JSTOR-stuff is now OCRed

Niels
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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Chris Goedde]

On Jun 22, 2007, at 11:40 AM, Adam R. Maxwell wrote:

>> 3) Can Bibdesk rename the pdfs when it moves/links them? For example,
>> I would like to have all my pdfs named CiteKey.pdf. Is that possible?
>> (This is a feature request.)
>>
>> 4) I can apparently customize the local-url. Why would I want to do
>> that?
>
> I think Niels answered these.

Yes, thanks to Niels and Christiaan for their answers. One thing I  
note is that in section 11.12 of the help (the AutoFile section) it  
never explicitly states that BibDesk will rename the file when it  
relocates it. Maybe this is obvious, but it wasn't to me. For  
example, this text:

File papers automatically: When you select this option, BibDesk will  
automatically move files into the papers folder hierarchy for new  
items. The new location will be build using a format string, which  
you can supply using the other controls. See AutoFile for more  
information about the Auto File feature.

could be augmented with a sentence saying that Bibdesk will fix the  
filename so that the local-url is correct. I know that's the way it  
*should* work, but it wasn't obvious that's the way that it *would*  
work. This page also seems to use the terms "path" and "location" in  
two different ways: sometimes to refer to the complete file url  
(including filename) and sometimes just to refer to the folder path.

Regarding Adam's question about what new users think, the issue for  
me wasn't whether BibDesk could keep track of pdfs, it was (a) why I  
would want to do this and (b) was BibDesk flexible enough/close  
enough to my way of thinking to be useful. For me, I think having a  
short quicktime movie that showed how things work would have been  
very helpful.

-- 
Chris Goedde


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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Adam R. Maxwell]

 
On Friday, June 22, 2007, at 10:04AM, "Alex Hamann" <[EMAIL PROTECTED]> wrote:
>
>Am 22.06.2007 um 17:03 schrieb Adam R. Maxwell:
>
>> You can also associate multiple files with
>> a single reference.
>
>follow up question here since I was not aware of this last option: Is  
>there a way of using AutoFile with associating multiple files with a  
>singel reference? 

AutoFile is tied to the Local-Url field.  I'm thinking of some modifications 
that may relax this (and store aliases instead of paths), but it will require a 
lot of new bugs^H^H^H^Hcode to be written.

-- 
Adam

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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Alex Hamann]

Am 22.06.2007 um 19:37 schrieb Alexander H. Montgomery:

>
> On Jun 22, 2007, at 9:43 AM, Alex Hamann wrote:
>
>>
>> Am 22.06.2007 um 17:03 schrieb Adam R. Maxwell:
>>
>>
> How are you guys handling your reference-materials?
>>
>> *snip
>>>
>>> I mainly have PDF files, with the odd HTML/PostScript/TIFF, all
>>> managed with BibDesk's AutoFile.  They're linked to references in
>>> BibDesk, since I'd go nuts using more than one program for the same
>>> task. One plus for BibDesk: it doesn't care what file format you
>>> attach, and you can search the contents of the attached files as  
>>> well
>>> as the reference metadata.  You can also associate multiple files
>>> with
>>> a single reference.
>>
>> follow up question here since I was not aware of this last option: Is
>> there a way of using AutoFile with associating multiple files with a
>> singel reference? If so, is there a special way I should modify my
>> current AutoFile
>> this is my current format string:
>>  %b/%p1/%f{Cite Key}%e
>>
>> Alex
>
> Option 1: Put multiple files in a folder, drop the folder onto Local-
> URL. The folder will be renamed, the contents won't.
> Option 2: Create multiple fields of type local-url, drop each file
> onto each separate field.
>
> -AHM
>

Thanks, I suspected something like this. Good to get confirmation,  
though ;-)


Alex



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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Ista Zahn]

On Jun 22, 2007, at 12:57 PM, Adam R. Maxwell wrote:

>
> On Friday, June 22, 2007, at 09:01AM, "Niels Kobschätzki"  
> <[EMAIL PROTECTED]> wrote:
>> On Jun 22, 2007, at 5:33 PM, Adam R. Maxwell wrote:
>>
>> How about building the web-site a way that it propagates the most
>> important/interesting features.
>>
>> I think about shorter texts with more highlights (e.g. bold letters
>> than 'text').
The features that a new user will find useful will depend on where  
they're starting from. If they don't have a pre-existing reference/ 
pdf collection, they will likely be interested in creating new  
references or importing them from searches. OTOH, I had an extensive  
collection of both references and pdfs that I needed to migrate from  
another system, so I was particularly interested in figuring out how  
to link a bunch of pdfs to the corresponding references (Claus  
Gerhardt helped me out with a very nice AppleScript--Thanks Claus!).  
The help file is already set up in an if-then sort of way (e.g., if  
you already know BibTex, read the quickstart, if you don't know  
BibTeX read the intro). Expanding on this approach such that new  
users can quickly find information on the features they need,  
depending on their situation, might be helpful for new users.

>
>> E.g. propagating auto-file through software: Activate it
>> automatically and give a warning window which can be switched off
>> (don't show this window again) or add some kind of assistant which
>> will give you the opportunity to switch features like this on or off
>> when you first start the program (and give the user the ability to
>> start it later again)
>
> I think the problem is that people don't even know you can add  
> files, though, so this wouldn't even make it discoverable.  What do  
> our newer users think?

As a new user coming from Sente, the add files feature was very  
intuitive--just drag and drop! Works just how you would expect.
>>


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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Alexander H. Montgomery]

On Jun 22, 2007, at 8:26 AM, Niels Kobschätzki wrote:

> On Jun 22, 2007, at 5:03 PM, Adam R. Maxwell wrote:
>
>>
>> On Jun 21, 2007, at 23:08, Niels Kobschätzki wrote:
>>
>>> On Jun 22, 2007, at 7:52 AM, Niels Kobschätzki wrote:
 I just found out that I could use iTunes for managing PDFs. It
 allows
>>> me to do a fast search on them (Genre: Papers; Artist: Author-Name;
>>> Title: Paper-name; Comments: Keywords) and they are organized in one
>>> place (iTunes-Music-library) which gets backed up regularly.
>>
>> I'm guessing it doesn't allow you to search by content, though?  It
>> really depends on what you need.
>
> Most of the "interesting" stuff is non-OCR-JSTOR-stuff anyway -- I
> gave up the illusion to search the content of my pdfs (and stuff in
> iTunes can be handled by Spotlight). Some kind of tagging and not
> thinking about the managing in the file-system is more important to  
> me.
>
> Niels

All of JSTOR is now OCRed. If you have the permanent URLs in  
BibDesk's URL field, you can use my JSTOR Download PDF script to grab  
the new versions, which are also smaller. (Warning: They are  
compressed with JBIG2, which Apple's PDFKit is slow at rendering)

http://people.reed.edu/~ahm/Projects/Citation/BibDesk/

Note that the script won't work through a proxy, only when you have  
direct campus access.

-AHMM
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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Alexander H. Montgomery]

On Jun 22, 2007, at 9:43 AM, Alex Hamann wrote:

>
> Am 22.06.2007 um 17:03 schrieb Adam R. Maxwell:
>
>
 How are you guys handling your reference-materials?
>
> *snip
>>
>> I mainly have PDF files, with the odd HTML/PostScript/TIFF, all
>> managed with BibDesk's AutoFile.  They're linked to references in
>> BibDesk, since I'd go nuts using more than one program for the same
>> task. One plus for BibDesk: it doesn't care what file format you
>> attach, and you can search the contents of the attached files as well
>> as the reference metadata.  You can also associate multiple files  
>> with
>> a single reference.
>
> follow up question here since I was not aware of this last option: Is
> there a way of using AutoFile with associating multiple files with a
> singel reference? If so, is there a special way I should modify my
> current AutoFile
> this is my current format string:
>   %b/%p1/%f{Cite Key}%e
>
> Alex

Option 1: Put multiple files in a folder, drop the folder onto Local- 
URL. The folder will be renamed, the contents won't.
Option 2: Create multiple fields of type local-url, drop each file  
onto each separate field.

-AHM

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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Christiaan Hofman]

On 22 Jun 2007, at 6:40 PM, Adam R. Maxwell wrote:

>
> On Friday, June 22, 2007, at 08:54AM, "Chris Goedde"  
> <[EMAIL PROTECTED]> wrote:
>> On Jun 22, 2007, at 10:33 AM, Adam R. Maxwell wrote:
>>
>> 2) Bibdesk keeps all the pdfs in a single folder, correct? Is it
>> possible to have a separate location for each bib file (question, not
>> feature request). I ask because of 1) above; I'm not sure I want to
>> mix all my pdfs if I continue to use separate bib files.
>
> You can use document info for this, I think, but Christiaan knows  
> more about it than I do.  I use the Group field to organize into  
> subfolders based on my old arrangement of files.
>

There are several ways. As Adam mentioned, you can use an (arbitrary)  
key in the Document Info. Just add something like:

%i{PapersFolder}/%f{CiteKey}%e

assuming that the document info key is called PapersFolder and the  
name of the file is the same as the cite key (apart from the extension).

Also, you can store papers relative to the .bib file rather than  
inside a fixed location.

Christiaan


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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Niels Kobschätzki]

On Jun 22, 2007, at 6:57 PM, Adam R. Maxwell wrote:

>
> On Friday, June 22, 2007, at 09:01AM, "Niels Kobschätzki"  
> <[EMAIL PROTECTED]> wrote:
>> On Jun 22, 2007, at 5:33 PM, Adam R. Maxwell wrote:
>>
>>>
>>> On Jun 22, 2007, at 08:26, Niels Kobschätzki wrote:
>>>
 I didn't know that this feature exists…cool…
>>>
>>> Aaargh!  I'm half convinced that people write new apps for  
>>> reference/
>>> PDF management because they don't know BibDesk can do this.  How can
>>> we advertise it more effectively?  I've been using it for years, and
>>> just assume that others use it as well.
>>
>> How about building the web-site a way that it propagates the most
>> important/interesting features.
>>
>> I think about shorter texts with more highlights (e.g. bold letters
>> than 'text').
>
> Me not understand HTML (and engineers make bad web designers,  
> anyway)!  I'd be happy to give shell access to anyone who wants to  
> take a shot at revamping things.  Most of the "manual" style  
> content should be moved to the wiki, I think (the entire manual is  
> online now, anyway), and the home page should be more feature/ 
> description oriented.

I can think about some stuff - some static HTML-pages should do it.  
But it would take some time because of other involvements right now.
Maybe there should be some brainstorming what the most interesting  
parts of BibDesk are which users should know about.
Big maybe as well: maybe there should be some merged page about Skim  
and BibDesk because I guess that a lot of ppl here are using both and  
at least the notes-part is available in both (could be a feature-to- 
mention as well)

>> E.g. propagating auto-file through software: Activate it
>> automatically and give a warning window which can be switched off
>> (don't show this window again) or add some kind of assistant which
>> will give you the opportunity to switch features like this on or off
>> when you first start the program (and give the user the ability to
>> start it later again)
>
> I think the problem is that people don't even know you can add  
> files, though, so this wouldn't even make it discoverable.  What do  
> our newer users think?

With an assistant that let's you know about this feature you would  
know ;)
The same when you drew a file to the local-URL-field (I found that  
rather fast) and auto-filing would be enabled per default and a  
dialogue when you use it the first time (until you switch off the  
dialogue)

>> Btw. I just searched 5 minutes for the auto-consolidate-command (I
>> expected it in File or in Database -- in the help it isn't mentioned
>> where it is. The help should mention those stuff . Instead of "Choose
>> this command to scan all selected publications in the file for linked
>> files. A dialog will be opened that asks you for some options. You
>> can find it in.", it would be better to have a sentence like this
>> "Choose auto-consolidate (Publication->Auto-Consolidate) to scan all
>> selected publications in the file for linked files. A dialog will be
>> opened that asks you for some options."
>
> Please file bug reports on the online help when you find that it's  
> not adequate.  Better yet, anyone who wants to improve it can have  
> commit access (I assume Mike and Christiaan agree to that :).  The  
> help book is written in GNU Texinfo, which is pretty easy to write.

Here's the same as for the html-stuff - I had to write FAQ-stuff for  
a webhoster and for the IT-department of one of the faculties of the  
university where I study.
But I would need some native who has a look over the texts (same for  
html) because I'm native German ;)



>
> When you do a search on your database, there's an option for "File  
> Content."  It indexes all attached files with Search Kit (closing  
> the document will lose the index, sadly, but it's very fast as long  
> as the index is in memory).

I found the File Content-option after to get to know that you can  
search file content ;)

Niels
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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Jason Davies]

>I think the problem is that people don't even know you can add files,
>though, so this wouldn't even make it discoverable.  What do our newer
>users think?

uh, was very obvious to me. don't even remember working it out, 
just started using it. but I didn't know about the file contents 
search thing.

My workflow (since it's workflow sharing day) is currently this:

1) new pdfs (they're virtually all pdfs) go into a folder which 
gets syncd to my palm for some reading in Documents To Go.

2) I skim them in DTG on the Palm, if interesting I then mark 
them for proper reading.

3) I read them in Acrobat Professional - my new toy - and 
highlight, add stickies etc. I note in Bibdesk whether I need to 
come back to them for the book I'm writing in the keywords.

4) once read and highlighted, save and move to an archive folder 
of unsorted PDFs. I give it the Bibtex name (davies04a) so I can 
find it easily later and add THAT location  in the Finder to 
bibdesk as a local URL. Annotations and abstracts also go into BibDesk.


I used to use Yojimbo but got the impression that it was not 
ideal for storing lots and lots of pdfs so moved to having them 
as Finder files.

Other abandoned workflows: Devonkthink (the entire range), 
Voodoopad (not ideal for archiving but a great product). And a 
very complex Filemaker database that never really worked.

currently I think it's working...


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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Alex Hamann]

Am 22.06.2007 um 17:03 schrieb Adam R. Maxwell:


>>> How are you guys handling your reference-materials?

*snip
>
> I mainly have PDF files, with the odd HTML/PostScript/TIFF, all
> managed with BibDesk's AutoFile.  They're linked to references in
> BibDesk, since I'd go nuts using more than one program for the same
> task. One plus for BibDesk: it doesn't care what file format you
> attach, and you can search the contents of the attached files as well
> as the reference metadata.  You can also associate multiple files with
> a single reference.

follow up question here since I was not aware of this last option: Is  
there a way of using AutoFile with associating multiple files with a  
singel reference? If so, is there a special way I should modify my  
current AutoFile
this is my current format string:
%b/%p1/%f{Cite Key}%e

Alex

>
>
> -- 
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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Jason Davies]

>Can you make it so that we can use it without reading any
>documentation? :-).

there is an entire section on this in the manual, IIRC.




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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Adam R. Maxwell]

 
On Friday, June 22, 2007, at 08:54AM, "Chris Goedde" <[EMAIL PROTECTED]> wrote:
>On Jun 22, 2007, at 10:33 AM, Adam R. Maxwell wrote:
>
>>
>> Aaargh!  I'm half convinced that people write new apps for reference/
>> PDF management because they don't know BibDesk can do this.  How can
>> we advertise it more effectively?  I've been using it for years, and
>> just assume that others use it as well.
>
>Can you make it so that we can use it without reading any  
>documentation? :-).

Well...sure, but it wouldn't be any different, because we (or I) don't know 
what is difficult about it.  Mike, Christiaan, and I wrote the bulk of the 
documentation, but most of the features are obvious to use, since we're 
familiar with the code.

>I'm just switching to Bibdesk (from many years of using BibView under  
>X11), and I have some questions. Some are related to autofile, some  
>are more general.
>
>1) Right now I keep my files in several bibliography file, but I've  
>been thinking of combining them into a single bib file. (This would  
>mean assigning them keywords to be able to sort them, I think.)  
>Recommendations? Pros/cons?

I merged my files into a single one, so it's easier to keep track of them.  My 
approach was to use a field named "Group", and assign a particular Group to 
each sub file.  This fits pretty well with the current features for 
sorting/grouping/searching.

>2) Bibdesk keeps all the pdfs in a single folder, correct? Is it  
>possible to have a separate location for each bib file (question, not  
>feature request). I ask because of 1) above; I'm not sure I want to  
>mix all my pdfs if I continue to use separate bib files.

You can use document info for this, I think, but Christiaan knows more about it 
than I do.  I use the Group field to organize into subfolders based on my old 
arrangement of files.

>3) Can Bibdesk rename the pdfs when it moves/links them? For example,  
>I would like to have all my pdfs named CiteKey.pdf. Is that possible?  
>(This is a feature request.)
>
>4) I can apparently customize the local-url. Why would I want to do  
>that?

I think Niels answered these.

Adam

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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Adam R. Maxwell]

 
On Friday, June 22, 2007, at 09:01AM, "Niels Kobschätzki" <[EMAIL PROTECTED]> 
wrote:
>On Jun 22, 2007, at 5:33 PM, Adam R. Maxwell wrote:
>
>>
>> On Jun 22, 2007, at 08:26, Niels Kobschätzki wrote:
>>
>>> I didn't know that this feature exists…cool…
>>
>> Aaargh!  I'm half convinced that people write new apps for reference/
>> PDF management because they don't know BibDesk can do this.  How can
>> we advertise it more effectively?  I've been using it for years, and
>> just assume that others use it as well.
>
>How about building the web-site a way that it propagates the most  
>important/interesting features.
>
>I think about shorter texts with more highlights (e.g. bold letters  
>than 'text').

Me not understand HTML (and engineers make bad web designers, anyway)!  I'd be 
happy to give shell access to anyone who wants to take a shot at revamping 
things.  Most of the "manual" style content should be moved to the wiki, I 
think (the entire manual is online now, anyway), and the home page should be 
more feature/description oriented.

>E.g. propagating auto-file through software: Activate it  
>automatically and give a warning window which can be switched off  
>(don't show this window again) or add some kind of assistant which  
>will give you the opportunity to switch features like this on or off  
>when you first start the program (and give the user the ability to  
>start it later again)

I think the problem is that people don't even know you can add files, though, 
so this wouldn't even make it discoverable.  What do our newer users think?

>Btw. I just searched 5 minutes for the auto-consolidate-command (I  
>expected it in File or in Database -- in the help it isn't mentioned  
>where it is. The help should mention those stuff . Instead of "Choose  
>this command to scan all selected publications in the file for linked  
>files. A dialog will be opened that asks you for some options. You  
>can find it in.", it would be better to have a sentence like this  
>"Choose auto-consolidate (Publication->Auto-Consolidate) to scan all  
>selected publications in the file for linked files. A dialog will be  
>opened that asks you for some options."

Please file bug reports on the online help when you find that it's not 
adequate.  Better yet, anyone who wants to improve it can have commit access (I 
assume Mike and Christiaan agree to that :).  The help book is written in GNU 
Texinfo, which is pretty easy to write.

>Nice that it says "Consolidate 5 files" when I chose 5 files but the  
>feature is called "auto-consolidate". Therefore it should be "auto- 
>consolidate" or "auto-consolidate 5 files" in the menu (I prefer the  
>first one - menu-items should be static imho and not dynamic except  
>for greying out stuff)
>
>>
>> True.  The disadvantage of Spotlight is that you can't limit the scope
>> of its search easily.  Regardless, I gave up organizing by hand in the
>> Finder, and now all searching is handled by BibDesk (metadata and
>> content).
>
>Bibdesk can search content? Good that I started this thread…
>I use Bibdesk now for over one year and those two features are really  
>really good…

When you do a search on your database, there's an option for "File Content."  
It indexes all attached files with Search Kit (closing the document will lose 
the index, sadly, but it's very fast as long as the index is in memory).

Adam

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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Niels Kobschätzki]

On Jun 22, 2007, at 5:53 PM, Chris Goedde wrote:

> On Jun 22, 2007, at 10:33 AM, Adam R. Maxwell wrote:
>
>>
>> Aaargh!  I'm half convinced that people write new apps for reference/
>> PDF management because they don't know BibDesk can do this.  How can
>> we advertise it more effectively?  I've been using it for years, and
>> just assume that others use it as well.
>
> Can you make it so that we can use it without reading any
> documentation? :-).
>
> I'm just switching to Bibdesk (from many years of using BibView under
> X11), and I have some questions. Some are related to autofile, some
> are more general.
>
> 1) Right now I keep my files in several bibliography file, but I've
> been thinking of combining them into a single bib file. (This would
> mean assigning them keywords to be able to sort them, I think.)
> Recommendations? Pros/cons?
>
> 2) Bibdesk keeps all the pdfs in a single folder, correct? Is it
> possible to have a separate location for each bib file (question, not
> feature request). I ask because of 1) above; I'm not sure I want to
> mix all my pdfs if I continue to use separate bib files.

You can change it that it creates different folders in a sub-folder

>
> 3) Can Bibdesk rename the pdfs when it moves/links them? For example,
> I would like to have all my pdfs named CiteKey.pdf. Is that possible?
> (This is a feature request.)

Yp - just play around with Preferences -> Autofile -> Local URL-Format
I use now: %a1/%Y/%T5 %f{Cite Key}%e (can be easily modified through  
menus in the preference)

Which gives something like:  archive-folder/author/year/title cite- 
key.pdf

> 4) I can apparently customize the local-url. Why would I want to do
> that?

See the above

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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Niels Kobschätzki]

On Jun 22, 2007, at 5:33 PM, Adam R. Maxwell wrote:

>
> On Jun 22, 2007, at 08:26, Niels Kobschätzki wrote:
>
>> On Jun 22, 2007, at 5:03 PM, Adam R. Maxwell wrote:
>>>



>>> I mainly have PDF files, with the odd HTML/PostScript/TIFF, all
>>> managed with BibDesk's AutoFile.  They're linked to references in
>>> BibDesk, since I'd go nuts using more than one program for the same
>>> task. One plus for BibDesk: it doesn't care what file format you
>>> attach, and you can search the contents of the attached files as  
>>> well
>>> as the reference metadata.  You can also associate multiple files
>>> with
>>> a single reference.
>>
>> I didn't know that this feature exists…cool…
>
> Aaargh!  I'm half convinced that people write new apps for reference/
> PDF management because they don't know BibDesk can do this.  How can
> we advertise it more effectively?  I've been using it for years, and
> just assume that others use it as well.

How about building the web-site a way that it propagates the most  
important/interesting features.

I think about shorter texts with more highlights (e.g. bold letters  
than 'text').
The features-sites right now are more like manuals than "commercials  
for the features (and no one reads the manual when he first browses  
the site - I'm usually a manual reader as well but rarely with  
software…in the Mac-world I have often the feeling that the most  
interesting stuff is already propagated through the software and/or  
the web-site of the software).

E.g. propagating auto-file through software: Activate it  
automatically and give a warning window which can be switched off  
(don't show this window again) or add some kind of assistant which  
will give you the opportunity to switch features like this on or off  
when you first start the program (and give the user the ability to  
start it later again)

Btw. I just searched 5 minutes for the auto-consolidate-command (I  
expected it in File or in Database -- in the help it isn't mentioned  
where it is. The help should mention those stuff . Instead of "Choose  
this command to scan all selected publications in the file for linked  
files. A dialog will be opened that asks you for some options. You  
can find it in.", it would be better to have a sentence like this  
"Choose auto-consolidate (Publication->Auto-Consolidate) to scan all  
selected publications in the file for linked files. A dialog will be  
opened that asks you for some options."
Nice that it says "Consolidate 5 files" when I chose 5 files but the  
feature is called "auto-consolidate". Therefore it should be "auto- 
consolidate" or "auto-consolidate 5 files" in the menu (I prefer the  
first one - menu-items should be static imho and not dynamic except  
for greying out stuff)

>
> I just found out that I could use iTunes for managing PDFs. It
> allows
 me to do a fast search on them (Genre: Papers; Artist: Author-Name;
 Title: Paper-name; Comments: Keywords) and they are organized in  
 one
 place (iTunes-Music-library) which gets backed up regularly.
>>>
>>> I'm guessing it doesn't allow you to search by content, though?  It
>>> really depends on what you need.
>>
>> Most of the "interesting" stuff is non-OCR-JSTOR-stuff anyway -- I
>> gave up the illusion to search the content of my pdfs (and stuff in
>> iTunes can be handled by Spotlight). Some kind of tagging and not
>> thinking about the managing in the file-system is more important to
>> me.
>
> True.  The disadvantage of Spotlight is that you can't limit the scope
> of its search easily.  Regardless, I gave up organizing by hand in the
> Finder, and now all searching is handled by BibDesk (metadata and
> content).

Bibdesk can search content? Good that I started this thread…
I use Bibdesk now for over one year and those two features are really  
really good…

Niels


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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Chris Goedde]

On Jun 22, 2007, at 10:33 AM, Adam R. Maxwell wrote:

>
> Aaargh!  I'm half convinced that people write new apps for reference/
> PDF management because they don't know BibDesk can do this.  How can
> we advertise it more effectively?  I've been using it for years, and
> just assume that others use it as well.

Can you make it so that we can use it without reading any  
documentation? :-).

I'm just switching to Bibdesk (from many years of using BibView under  
X11), and I have some questions. Some are related to autofile, some  
are more general.

1) Right now I keep my files in several bibliography file, but I've  
been thinking of combining them into a single bib file. (This would  
mean assigning them keywords to be able to sort them, I think.)  
Recommendations? Pros/cons?

2) Bibdesk keeps all the pdfs in a single folder, correct? Is it  
possible to have a separate location for each bib file (question, not  
feature request). I ask because of 1) above; I'm not sure I want to  
mix all my pdfs if I continue to use separate bib files.

3) Can Bibdesk rename the pdfs when it moves/links them? For example,  
I would like to have all my pdfs named CiteKey.pdf. Is that possible?  
(This is a feature request.)

4) I can apparently customize the local-url. Why would I want to do  
that?

Thanks,

Chris Goedde




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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Etienne Roesch]

Hi all,

Hereafter part of a post I sent a few weeks ago. Hope this helps.

"For info, my workflow is as follows: BibDesk (ref hunting, pdf  
handling, bib storing) + Journler ( sorting/ 
tagging of notes and research resources, pdf, graphs, etc) + iGTD  
( getting-things-done app). The core of  
the workflow is Journler which gets info from both BibDesk and iGTD,  
using applescript for the former and the built-in url features in the  
latter.


The applescript part detects whenever a new pub is added to my main  
filed-by-BibDesk publication folder, takes it, creates a new item in  
Journler (adding an alias to it), and tags it (the file, not only the  
entry) as "processed" to ease troubleshooting, if ever. I posted the  
applescript there : ."



Le 22 juin 07 à 07:52, Niels Kobschätzki a écrit :


Hi!

Once again I'm thinking about how to handle all my reference
material. Right now I'm using Yojimbo to get all the website-stuff
from the net and then there are PDFs.
For handling PDFs I see at time three options:
a) Using the Finder with metatags and some good file names (any
suggestions for conventions)
b) Using DevonThink Personal (I've got a license for it from MacZot
and the other versions are just too expensive for me right now)
c) Using Papers (just downloading the actual version)

I would use BibDesk in all three cases because I write all my stuff
with LaTeX and I think it's superior if it comes to handling bib- 
files.

In the end all files should be in some system where I can easily find
and manage them.

How are you guys handling your reference-materials?

Niels

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-
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Geneva Emotion Research Group
University of Geneva (Office 5137) - Bd du Pont d'Arve 40
1205 Geneva - SWITZERLAND
Tel/Fax: +41 (0)22 379 92 27/19 - Cell: +41 (0)79 773 62 93
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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Adam R. Maxwell]

On Jun 22, 2007, at 08:26, Niels Kobschätzki wrote:

> On Jun 22, 2007, at 5:03 PM, Adam R. Maxwell wrote:
>
>>
>> On Jun 21, 2007, at 23:08, Niels Kobschätzki wrote:
>>
>>> On Jun 22, 2007, at 7:52 AM, Niels Kobschätzki wrote:
>>>
 Hi!

 Once again I'm thinking about how to handle all my reference
 material. Right now I'm using Yojimbo to get all the website-stuff
 from the net and then there are PDFs.
 For handling PDFs I see at time three options:
 a) Using the Finder with metatags and some good file names (any
 suggestions for conventions)
 b) Using DevonThink Personal (I've got a license for it from MacZot
 and the other versions are just too expensive for me right now)
 c) Using Papers (just downloading the actual version)

 I would use BibDesk in all three cases because I write all my stuff
 with LaTeX and I think it's superior if it comes to handling bib-
 files.
 In the end all files should be in some system where I can easily
 find and manage them.

 How are you guys handling your reference-materials?
>>
>> I mainly have PDF files, with the odd HTML/PostScript/TIFF, all
>> managed with BibDesk's AutoFile.  They're linked to references in
>> BibDesk, since I'd go nuts using more than one program for the same
>> task. One plus for BibDesk: it doesn't care what file format you
>> attach, and you can search the contents of the attached files as well
>> as the reference metadata.  You can also associate multiple files  
>> with
>> a single reference.
>
> I didn't know that this feature exists…cool…

Aaargh!  I'm half convinced that people write new apps for reference/ 
PDF management because they don't know BibDesk can do this.  How can  
we advertise it more effectively?  I've been using it for years, and  
just assume that others use it as well.

 I just found out that I could use iTunes for managing PDFs. It
 allows
>>> me to do a fast search on them (Genre: Papers; Artist: Author-Name;
>>> Title: Paper-name; Comments: Keywords) and they are organized in one
>>> place (iTunes-Music-library) which gets backed up regularly.
>>
>> I'm guessing it doesn't allow you to search by content, though?  It
>> really depends on what you need.
>
> Most of the "interesting" stuff is non-OCR-JSTOR-stuff anyway -- I
> gave up the illusion to search the content of my pdfs (and stuff in
> iTunes can be handled by Spotlight). Some kind of tagging and not
> thinking about the managing in the file-system is more important to  
> me.

True.  The disadvantage of Spotlight is that you can't limit the scope  
of its search easily.  Regardless, I gave up organizing by hand in the  
Finder, and now all searching is handled by BibDesk (metadata and  
content).

-- 
Adam
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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Niels Kobschätzki]

On Jun 22, 2007, at 5:03 PM, Adam R. Maxwell wrote:

>
> On Jun 21, 2007, at 23:08, Niels Kobschätzki wrote:
>
>> On Jun 22, 2007, at 7:52 AM, Niels Kobschätzki wrote:
>>
>>> Hi!
>>>
>>> Once again I'm thinking about how to handle all my reference
>>> material. Right now I'm using Yojimbo to get all the website-stuff
>>> from the net and then there are PDFs.
>>> For handling PDFs I see at time three options:
>>> a) Using the Finder with metatags and some good file names (any
>>> suggestions for conventions)
>>> b) Using DevonThink Personal (I've got a license for it from MacZot
>>> and the other versions are just too expensive for me right now)
>>> c) Using Papers (just downloading the actual version)
>>>
>>> I would use BibDesk in all three cases because I write all my stuff
>>> with LaTeX and I think it's superior if it comes to handling bib-
>>> files.
>>> In the end all files should be in some system where I can easily
>>> find and manage them.
>>>
>>> How are you guys handling your reference-materials?
>
> I mainly have PDF files, with the odd HTML/PostScript/TIFF, all
> managed with BibDesk's AutoFile.  They're linked to references in
> BibDesk, since I'd go nuts using more than one program for the same
> task. One plus for BibDesk: it doesn't care what file format you
> attach, and you can search the contents of the attached files as well
> as the reference metadata.  You can also associate multiple files with
> a single reference.

I didn't know that this feature exists…cool…

>
>>> I just found out that I could use iTunes for managing PDFs. It  
>>> allows
>> me to do a fast search on them (Genre: Papers; Artist: Author-Name;
>> Title: Paper-name; Comments: Keywords) and they are organized in one
>> place (iTunes-Music-library) which gets backed up regularly.
>
> I'm guessing it doesn't allow you to search by content, though?  It
> really depends on what you need.

Most of the "interesting" stuff is non-OCR-JSTOR-stuff anyway -- I  
gave up the illusion to search the content of my pdfs (and stuff in  
iTunes can be handled by Spotlight). Some kind of tagging and not  
thinking about the managing in the file-system is more important to me.

Niels 
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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Adam R. Maxwell]

On Jun 21, 2007, at 23:08, Niels Kobschätzki wrote:

> On Jun 22, 2007, at 7:52 AM, Niels Kobschätzki wrote:
>
>> Hi!
>>
>> Once again I'm thinking about how to handle all my reference
>> material. Right now I'm using Yojimbo to get all the website-stuff
>> from the net and then there are PDFs.
>> For handling PDFs I see at time three options:
>> a) Using the Finder with metatags and some good file names (any
>> suggestions for conventions)
>> b) Using DevonThink Personal (I've got a license for it from MacZot
>> and the other versions are just too expensive for me right now)
>> c) Using Papers (just downloading the actual version)
>>
>> I would use BibDesk in all three cases because I write all my stuff
>> with LaTeX and I think it's superior if it comes to handling bib-
>> files.
>> In the end all files should be in some system where I can easily
>> find and manage them.
>>
>> How are you guys handling your reference-materials?

I mainly have PDF files, with the odd HTML/PostScript/TIFF, all  
managed with BibDesk's AutoFile.  They're linked to references in  
BibDesk, since I'd go nuts using more than one program for the same  
task. One plus for BibDesk: it doesn't care what file format you  
attach, and you can search the contents of the attached files as well  
as the reference metadata.  You can also associate multiple files with  
a single reference.

>> I just found out that I could use iTunes for managing PDFs. It allows
> me to do a fast search on them (Genre: Papers; Artist: Author-Name;
> Title: Paper-name; Comments: Keywords) and they are organized in one
> place (iTunes-Music-library) which gets backed up regularly.

I'm guessing it doesn't allow you to search by content, though?  It  
really depends on what you need.

-- 
Adam


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Re: [Bibdesk-users] [OT] Workflow for handling reference-materials

[Niels Kobschätzki]

On Jun 22, 2007, at 7:52 AM, Niels Kobschätzki wrote:

> Hi!
>
> Once again I'm thinking about how to handle all my reference  
> material. Right now I'm using Yojimbo to get all the website-stuff  
> from the net and then there are PDFs.
> For handling PDFs I see at time three options:
> a) Using the Finder with metatags and some good file names (any  
> suggestions for conventions)
> b) Using DevonThink Personal (I've got a license for it from MacZot  
> and the other versions are just too expensive for me right now)
> c) Using Papers (just downloading the actual version)
>
> I would use BibDesk in all three cases because I write all my stuff  
> with LaTeX and I think it's superior if it comes to handling bib- 
> files.
> In the end all files should be in some system where I can easily  
> find and manage them.
>
> How are you guys handling your reference-materials?

I just found out that I could use iTunes for managing PDFs. It allows  
me to do a fast search on them (Genre: Papers; Artist: Author-Name;  
Title: Paper-name; Comments: Keywords) and they are organized in one  
place (iTunes-Music-library) which gets backed up regularly.
What do you think?

Niels
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