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Organize pdfs on your HDD


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6 replies to this topic

#1 noelmathur

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Posted 19 October 2009 - 03:10 AM

Hello folks,

I searched for my question on the forum and didn't find any similar question posted.

My goal is,
1. Organize all the pdfs on local HDD.
2. Be able to make folders in the program to organize the reference and pdf attached to it.
3. The program should be able to download the pdf automatically, (of course, from the journal websites our university subscribes) and links it to the reference in the program.
4. Allows tagging.
5. Mac program (I welcome PC alternatives too that I can use at home)
6. I don't care about bibliography creation out of this program, we have endnote for that.

I have tried Mendeley and iPapers. I didn't like Mendeley. iPapers2 is a good program but I face few glitches that I can't figure out, like it fails to download the article thats free from pubmed !!
Zotero is an option I could think of but I don't know if it downloads pdfs automatically. Its new 2.0 version is still in beta so will have to wait till final version for pubmed use.
I liked Papers but its shareware and we are not allowed to install anything thats not approved by the university. I thought I could run Papers from the USB stick but I don't know what files it leaves on local HDD. Hence don't want to take chances.

Which program do you suggest?

Thank you very much.

#2 Dr. Gunn

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Posted 19 October 2009 - 07:41 AM

Hello folks,

I searched for my question on the forum and didn't find any similar question posted.

My goal is,
1. Organize all the pdfs on local HDD.
2. Be able to make folders in the program to organize the reference and pdf attached to it.
3. The program should be able to download the pdf automatically, (of course, from the journal websites our university subscribes) and links it to the reference in the program.
4. Allows tagging.
5. Mac program (I welcome PC alternatives too that I can use at home)
6. I don't care about bibliography creation out of this program, we have endnote for that.

I have tried Mendeley and iPapers. I didn't like Mendeley. iPapers2 is a good program but I face few glitches that I can't figure out, like it fails to download the article thats free from pubmed !!
Zotero is an option I could think of but I don't know if it downloads pdfs automatically. Its new 2.0 version is still in beta so will have to wait till final version for pubmed use.
I liked Papers but its shareware and we are not allowed to install anything thats not approved by the university. I thought I could run Papers from the USB stick but I don't know what files it leaves on local HDD. Hence don't want to take chances.

Which program do you suggest?

Thank you very much.


Noel, you say you've tried Mendeley and didn't like it, but have you tried it recently? The mac version, particularly, has been much improved.

#3 hobglobin

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Posted 19 October 2009 - 08:40 AM

Have a look here

One must presume that long and short arguments contribute to the same end. - Epicurus
...except casandra's that belong to the funniest, most interesting and imaginative (or over-imaginative?) ones, I suppose.

That is....if she posts at all.


#4 noelmathur

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Posted 19 October 2009 - 09:23 AM

Thanks for your resplies.

@hobglobin,
I have already looked at this comparison but don't have time to check each and everyone so I am looking for preference that folks have so that I would give a try to only those ones and see which one fits my needs best.

#5 noelmathur

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Posted 19 October 2009 - 10:28 PM

Noel, you say you've tried Mendeley and didn't like it, but have you tried it recently? The mac version, particularly, has been much improved.

Dr. Gunn,
I am just trying Mendeley but there is not too much of improvement.
- Still you can not directly import from pubmed, like Papers does (MAJOR drawback)
- It doesn't allow you to rename the files as you wish (even after checking button for rename the files, no changes can be made)

Honestly, papers still rocks. I just hope, I get green light to install it on my machine and I wouldn't even look at the other programs. Since I am not looking for bibliographic ability, papers is great for my work.

#6 Dr. Gunn

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Posted 20 October 2009 - 09:09 AM

Noel, you say you've tried Mendeley and didn't like it, but have you tried it recently? The mac version, particularly, has been much improved.

Dr. Gunn,
I am just trying Mendeley but there is not too much of improvement.
- Still you can not directly import from pubmed, like Papers does (MAJOR drawback)
- It doesn't allow you to rename the files as you wish (even after checking button for rename the files, no changes can be made)

Honestly, papers still rocks. I just hope, I get green light to install it on my machine and I wouldn't even look at the other programs. Since I am not looking for bibliographic ability, papers is great for my work.


Thanks for that feedback, Noel. Mendeley has a bookmarklet which you can use at publisher's sites and pubmed to automatically retrieve the citation information.

I'm not quite sure what you're having trouble with as far as renaming. Perhaps the renamed files are also being moved to a different directory and you're looking at the unrenamed, unmoved copies? I know that sounds obvious, but just wanted to rule that out first.

Edited by Dr. Gunn, 20 October 2009 - 10:26 AM.


#7 chromatin

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Posted 02 October 2010 - 08:59 PM

Try this:http://mekentosj.com/papers/
http://www.bioprotocols.info




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