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edub23o3

macrumors newbie
Feb 8, 2007
16
0
Milwaukee, WI
An update was just released for Papers to address the importing and matching of pdf's. The capability to export the library to BibTeX, Endnote and RIS was also added in this version. Starting out in the Phd program, I am glad to have this app to easily organize all the journal articles.
 

mkrishnan

Moderator emeritus
Jan 9, 2004
29,776
15
Grand Rapids, MI, USA
Can I ask anyone using Papers a question?

Suppose you already have a PDF... heh, of course you do. I have ... maybe 700-900 PDFs between my iMac and iBook. How easy is it to take the existing PDF and match it to a pubmed or psycarticles or whatever entry so that its fields can be populated in Papers?

Thank ya! :)
 

nsbio

macrumors 6502a
Aug 8, 2006
634
0
NC
How about the Ape plasmid editor?

http://www.biology.utah.edu/jorgensen/wayned/ape/

Free, cross-platform, and extremely useful for constructing plasmids, restriction digests etc. For me it replaced the old classic - the DNA strider - and that says a lot, since not one piece of numerous commercial bloatware has been able to match DNA strider in simplicity of use and functionality. Ape does it gratis.
 

smueboy

macrumors 6502a
Original poster
Oct 30, 2006
778
1
Oz
..How easy is it to take the existing PDF and match it to a pubmed or psycarticles or whatever entry so that its fields can be populated in Papers?..

Well, in public preview 1, i would drag my pdfs into Papers and then 'match' each one, one at a time as they were imported - typing in a couple of author names and a word or two from the title makes it very fast and easy to bring up the correct ref in PubMed (plus the preview pane allows you to see the pdf as you import).
Now that preview 2 is out, you import your pdf's and then match them (still individually) afterwards - though still in the same manner by searching pubmed. Sure, you can now add whole folders of pdf's, but you need to select each one to match it, rather than matching each one as they are imported. I'm yet to decide if the new method is easier or harder.
All in all though, it is time consuming, particularly when you have hundreds of pdf's, but once your database is up and running adding new pdfs daily or weekly should be pretty easy.
.
 

mkrishnan

Moderator emeritus
Jan 9, 2004
29,776
15
Grand Rapids, MI, USA
Well, in public preview 1...

Thank you for the detailed explanation (and also edub23o3). This answers my question completely. I wasn't sure if the fact that I did not "get" the document from Pubmed while inside Papers would make it much harder. I could see doing this. If it takes only ~20-30 seconds per doc, I can certainly do five a day until I have them all done.

Two more questions? :eek:

Right now, I have my PDFs organized à la "Krishnan - Depression and CVD meds.pdf" -- just first author + summary of title. This works great, and between that and spotlight, I do actually find files fairly quickly and reliably. However, I have about ~700 files each on my iBook and my iMac, with another 200 files on a share drive at school, not all of which are completely overlapping.

So... is it good at finding/managing/eliminating duplicates?

And how does it work for syncing between two different computers?
 

smueboy

macrumors 6502a
Original poster
Oct 30, 2006
778
1
Oz
Their release notes say that the functions for finding/managing duplicates are not implemented as yet (but will be).

Syncing - actually, what papers does is copy the pdfs to a folder in the Users>Documents folder. I haven't decided what i think about that yet - whether i will keep or delete all of my existing pdf's once i have copied them into Paper's (Obviously, for now i will until it's out of beta and working well for me, but in the end i may just back them up on a DVD).

Hope this helps.
 

mkrishnan

Moderator emeritus
Jan 9, 2004
29,776
15
Grand Rapids, MI, USA
I did download it just now. And thank you so much for your help. It seems fairly interesting. I guess I should probably get all my journal articles together, burn a DVD of the 800 or 900 or however many there end up being, and then start importing them, if I decide I'm sticking with this, since the import will be destructive to the filename system I'm using.
 

edub23o3

macrumors newbie
Feb 8, 2007
16
0
Milwaukee, WI
I was worried about changing the file names, but when you search in spotlight it shows the first few words of the title after the numeric pdf title. I will probably stick to the smart groups within papers to keep everythign organized.
 

mkrishnan

Moderator emeritus
Jan 9, 2004
29,776
15
Grand Rapids, MI, USA
Thanks -- my problem is that I use the files not only on my two Macs that have Spotlight but also on a number of department Windows computers (using a department share drive) and my WM5 PDA. So... while I have always loved how both iTunes and iPhoto manage my files for me, Papers just doesn't work for me. But it is a cute app. Nice concept.
 

Fiveos22

macrumors 65816
Nov 20, 2003
1,080
1
For those outside the beta-field of research (epidemiology for instance), it would be worthwhile to check out http://www.r-project.org/. R is an open source programme that can do pretty much everything SPSS can handle....for free. There's an OSX version as well.


We were required to use this for our life sciences stats class in college...if you can get used to its commands, R is ridiculously powerful.

Its been almost a year since I've been in a research lab, but when I was working on my thesis project I needed an analyzer to pick primers for RNAi work and found this little freebie: iRNAi. I don't know when it was last updated, but it probably works just as well as before.
 

shwc

macrumors regular
Jul 2, 2005
205
1
some more useful Apps

MacPymol:
incentive/donation ware
Simply amazing!! High end molecular viewer and much more.
http://pymol.sourceforge.net/

Papers, 4peaks, enzymeX, lab assistant:
All are Freeware, except for the low cost Papers
All are simply amazing!!
http://mekentosj.com/programs/

Sequence Analysis:
donationware
restriction digests, ORFs, hydrophobicity, and much more.
http://informagen.com/SA/

BioX
Freeware
Very helpful ... and destined to be very powerful.
A fantastic start ... a mac os X GUI interface to the ebiotools/emboss tools. Only some of tools are accesible by the mac GUI. The remainder are accessble by X-window interface.
http://www.lagercrantz.ath.cx/software/biox/

ipapers
Freeware
http://homepage.mac.com/toshihiro_aoyama/iPapers/

Osirix
Freeware
DICOM Viewer (not my field of study, but a truly amazing program)
http://homepage.mac.com/rossetantoine/osirix/

CLC free workbench:
Freeware
restriction digests, ORFs, hydrophobicity, and much more.
http://www.clcbio.com/free/

jchempaint
Freeware
http://sourceforge.net/project/showfiles.php?group_id=20024
http://almost.cubic.uni-koeln.de/cdk/jcp

Pro Fit (commercial program, pricey but good)
a powerful graphing and curve fitting program
http://www.quansoft.com/

Bookends (commercial program, costs $$, great value)
bibliography software
http://www.sonnysoftware.com/

Reference Miner
Freeware
http://www.sonnysoftware.com/

Mellel (commercial program, costs $$, great value)
A great word processor
http://www.redlers.com/

Fink
Freeware
Fink is a fairly painless way to get access to many scientific unix apps
http://fink.sourceforge.net/

MacVector (commercial program, costs lots and lots of $$)
http://www.accelrys.com/products/macvector/

Sequencher (commercial program, costs lots and lots of $$)
http://www.sequencher.com

Tnimage
Freeware
X-window based densitometry program
http://brneurosci.org/tnimage.html


BTW, Does anyone know of a decent (native) mac os X application for gel analysis? Note: I do not like imageJ.

--- Cheers.
--- Shwc.
 

edub23o3

macrumors newbie
Feb 8, 2007
16
0
Milwaukee, WI
Papers 1.0 released

Just received the email that Papers 1.0 was released. Haven't had a chance to check out the new features, but every new release so far has been a major improvement from the previous releases.
 

smueboy

macrumors 6502a
Original poster
Oct 30, 2006
778
1
Oz
Yeah - it looks very nice.

They have improved the way PDF's are imported - where they are stored (including across different computers) and how they are named etc. is now customisable. I like that i can keep all of my PDF's in the folders they are currently arranged in, without Papers needing to make a copy of them.

Matching pdf's also seems to be improved in Version 1.0. Now i just wish it could automatically import and match all of my files...
 

mkrishnan

Moderator emeritus
Jan 9, 2004
29,776
15
Grand Rapids, MI, USA
They have improved the way PDF's are imported - where they are stored (including across different computers) and how they are named etc. is now customisable. I like that i can keep all of my PDF's in the folders they are currently arranged in, without Papers needing to make a copy of them.

Wow, thank you! This is what I had been wanting... when you say that it can customize the names it uses, can it use a format like this:

First-Author's-Last-Name - Title.pdf

That would be ideal for me. Perhaps I need to take a second look at this app.
 
So does Papers actually offer any export (e.g. bib or EndNote / RefMan for compaitibility with Windows users) or cite-while-you-write functionality?

It looks nice but it is dead in the water, certainly for me, if it is only any good for putting stuff in. Getting it out, both quickly and in the right format, is the most important thing for any manager of this sort.

Another, highly desirable, feature would be integrated OCR so that imaged PDFs can be archived and indexed. I don't know of anything that does this right now, but I have a lot of older papers that have been archived as scanned images.
 

smueboy

macrumors 6502a
Original poster
Oct 30, 2006
778
1
Oz
Wow, thank you! This is what I had been wanting... when you say that it can customize the names it uses, can it use a format like this:

First-Author's-Last-Name - Title.pdf

That would be ideal for me. Perhaps I need to take a second look at this app.

yep. See attached prefs pane.


So does Papers actually offer any export (e.g. bib or EndNote / RefMan for compaitibility with Windows users) or cite-while-you-write functionality?

It looks nice but it is dead in the water, certainly for me, if it is only any good for putting stuff in. Getting it out, both quickly and in the right format, is the most important thing for any manager of this sort.

Another, highly desirable, feature would be integrated OCR so that imaged PDFs can be archived and indexed. I don't know of anything that does this right now, but I have a lot of older papers that have been archived as scanned images.

It offers export to BibTex, Endnote etc. That said, i still use Endnote to CWYW, and i use Papers as a readily searchable database of my papers, which is great when looking for certain refs while writing etc.

It can also import any pdf file - scanned or otherwise. You simply need to match the file to the pubmed reference.
 

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koobcamuk

macrumors 68040
Oct 23, 2006
3,195
9
can Papers use google scholar yet? I get all my papers from there and would love it if I could use that to search for them - not many in my field are published in PubMed.

Maybe if we can all email the developers and ask them to do it?
 

smueboy

macrumors 6502a
Original poster
Oct 30, 2006
778
1
Oz
Hmm.. i just opened Papers and got a message saying there was a new version. I first thought it was an error, but indeed there is now Papers 1.0.1 which apparently fixes some bugs.
 

mkrishnan

Moderator emeritus
Jan 9, 2004
29,776
15
Grand Rapids, MI, USA
can Papers use google scholar yet? I get all my papers from there and would love it if I could use that to search for them - not many in my field are published in PubMed.

Maybe if we can all email the developers and ask them to do it?

I think this is a fair point for them, but I'm also guessing that the problem will be that Google Scholar is too chaotic to get along with an engine like this, at least in its current form -- it generates hits on all kinds of weird stuff that may or may not actually exist or be accessible, and it tends to generate hundreds of different hits for the same material. In contrast, the major engines like PubMed and PsycInfo generate pretty standardized search results in a structured format.... So I'm guessing it would be very tough. Also presumably, since PubMed has hooks to download electronic citations with the organized information and abstract in them, that Papers is using this, and it would be difficult for them to re-make this out of Google Scholar.

Doesn't hurt to ask. But maybe if you instead or also recommend a major standard engine for your field? Most of the big fields have something like PubMed or PsycInfo that's the most accepted index in the field. I remember when I was in engineering that this was also true for engineering, although I don't remember the name anymore.
 

AmbitiousLemon

Moderator emeritus
Nov 28, 2001
3,415
3
down in Fraggle Rock
can Papers use google scholar yet? I get all my papers from there and would love it if I could use that to search for them - not many in my field are published in PubMed.

Maybe if we can all email the developers and ask them to do it?

Agreed. Looks great, but it can't import pdfs from endnote and it can only search pubmed. Add in web of knowledge and they get all science not just medical biology.
 
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