32 replies to this topic

[kokoro]

Hello hello,

I hope everyone's enjoying the summer!!

I needed some opinions about how to keep myself and these papers organized, and would appreciate any help.
In particular I was hoping for some sort of software to keep me on track, but again any suggestions will be greatly appreciated.

I'm a first year Grad Student and I spend a good deal of time reading to just basically catch-up, so I'm getting to the point where I've got piles of papers on my desk which I strongly feel I should do something about. For now, papers are separated topic-wise (revolving around NF-kB and the numerous tangents that can be drawn from it)... and that's probably about it... papers have read-unread marks on them, a few notes, and they are just piled high

Just looking ahead, I know I'm going to have trouble revisiting and finding some of these articles. Is an Excel file plausible?
Let me know what you guys do with what you read. My supervisor is able to sort what he needs from the trash, but you know, I'm not anywhere near that stage... and besides, I am for the most part focusing on major journals... so there isn't anything that's screaming to be thrown out

Thank you guys,
anderson

[Doki]

Use some reference manager software. I use zotero which is add-on for our fav browser Mozilla. It's very easy then. I just pile up my printed materials alphabetically. .  . Forget excel for now. Reference manager is not optional . . once you start writing papers, it will be so easy to insert the citations.. .

There are other commercial softwares also. .  many of them. Everyone I know use Endnote. Ask in the lab. They might have the software. Consult your senior who will show you how to use them. If you are using zotero then there is no pain. There are online reference libraries also like citeulike. It can be another good option.

Happy reading.

[hobglobin]

Here is a comparison of reference managing software from wikipedia...I use Reference Manager, but I'm not really lucky with it (but here I get it free). Openoffice has also a build-in database for references, perhaps I'll try out this, don't know how good it is

Edited by hobglobin, 12 August 2009 - 08:26 AM.

[fishdoc]

I've used Reference Manager and Endnote.

I started writing my dissertation using Microsoft Word with Endnote and Cite While You Write (there's a good toolbar in Word for Endnote), but then my advisor requested that I use WordPerfect. Endnote doesn't provide CWYW capability in WordPerfect, so I switched to Reference Manager. Along with some annoyances from WordPerfect, Reference Manager also had a few bugs that I didn't like and couldn't work around, so I migrated back to Endnote and Word. I think Endnote is a little more difficult to use (but not a lot), but has more ability to control your bibliographies and other things.

[kokoro]

thank you you guys

I will make sure to look into all that you've suggested  

[Rsm]

I don't know if you want to write and cite an article or just keep your PDF files organized. For organization I use iPapers (click), which is for free (but unfortunately only for Mac). But a lot easier than Endnote...
Cheers,
Minna

[HomeBrew]

You may also want to take a look at Mendeley.

[seanspotatobusiness]

My system:

I use the Zotero Firefox extension (mentioned above).

I save articles as PDF files in a folder, using the pubmid ID number as the file name.

I link all the PDF files to their respective records in Zotero.

I used PDFXchange viewer to highlight important passages in the text, annotate with my thoughts etc (it's much more flexible than Adobe Acrobat Reader). I often read articles on paper, then transfer the annotations, highlights etc to the version on my PC and dispose of (preferably recycle!) the paper version.


One of the great things about Zotero is that it can index all the PDF files (and I think other kinds of file) that you link to its records. Thus, suppose you read an article but can't remember what it was called, but do remember a few words or phrases - you type them into Zotero, and it lists the matches. There are loads of things which make it so much better than EndNote but I don't have time to get into it right now.

[Gideon]

kokoro, on Aug 12 2009, 07:29 PM, said:

thank you you guys

I will make sure to look into all that you've suggested  

Hi there, seems that many people have already suggested to you many different softwares. Probably to add on to what they have said, I think you should choose a software to suit your field of study. I use a free software called WizFolio. I am very satisfied with it so far and will strongly recommend to people writing scientific articles. You can sign up for a free account at www.wizfolio.com and give it a try:) Hope this helps!!!

[fluffybunny]

hi kokoro,

i use the traditional way. seems to me you print out all your articles and arrange according to topics. I buy bigfile them up according to topics. Then i arrange all the articles according to alphabetical order. Notes are made on the first page of the article consisting a summary of the article (one or two sentence). The article is dated to when I downloaded them off the internet (to ease my cross-referencing to my articles folder in the computer), and a 'check' to state that I've quoted this article in my writing.

Hope this helped good luck!

[jajell]

Could not have written my thesis without zotero!  Was a life saver.

[Radish]

Hi to you all

I use evernote, it allows you to store all your articles, notes lab results, and all I need to access them is internet.

Before that I used to use Papers from Mac.

[toejam]

i was using zotero until i came with the problem that i couldn't synchronize my library on different computers (as it is in my lab). if you're using only one computer, and i should also remark, and you do your writing on only one operating system (this is for the people who dual boot, since referencing has problems if you're swapping between openoffice / msoffice) then zotero is great.

fortunately my university provides us with endnote web, so i don't worry about that anymore. i know zotero 2.0 can manage synchronization but i haven't tried that, and probably won't. when products are still on beta testing it means it all can be ruined if you click on the wrong moment.

[susie]

We take a different approach allowing you both to manage your papers and keep them in context to the project. BioKM (www.biodata.com) is not a reference manager per se but we get good feedback from our users, It would be interesting to learn how well BioKM™ plays into your workflow with the previous mentioned ref managers.

Read more about how BioKM helps you manage your reference papers here.

[PandaCreamPuff]

I do think Zotero is the superior software but then you can only use it in Firefox right?

I am using one of the latest versions of EndNote and it allows you to do Pubmed searches WITHIN the software, and drag your results straight into your customised folders. Since I still prefer reading papers from hard copies, I print out the papers and alphabetically sort them according to topics.