We have internet! After paying a mere $15 to the cable modem company for the privilege of installing it ourselves (rather than $55 to have a service person visit), two phone calls to said cable company to troubleshoot the connection, and one close examination of our residence to find the well-hidden cable inlet (inside a cabinet; this might not have been so difficult had there not been three decoy cables in other locations), we are once again riding the tidal wave of misinformation.
Two weeks ago, Nature had an article about PDF archiving (you'll need a subscription to read it). They pointed to the program Papers; comments (which you can read w/o subscription) also pointed to various other solutions: google desktop, Sente, Zotero, Mac Spotlight, etc.
The commenter that made me laugh the most was the one who said he uses mind mapping software. I thought this was a joke until I googled it.
To date I have not bothered keeping PDFs on my computer, for some of the reasons listed in the article--it's impossible to come up with a naming system that is both consistent and consistently useful; hard to organize, etc. Also for another reason, which is that I much prefer reading paper than computer screens, so if I'm just going to print the paper out anyhow, what's the point in indexing it all complicated-like on my computer?
However, I can see the advantage of being able to organize and search through pdfs, since I'm quite bad at remembering papers I've read in any but the haziest form ("You know, that group, I think they're in Canada somewhere, they did something where they looked at the floogly-flugs, or maybe it was at the poogly-plugs, now I'm not sure, but the result was that they changed during development, only now I don't remember if they increased or decreased"). Also, mind-mapping dude's comment about attaching ideas to articles made some goofy sense to me.
I have a reasonably good organization system for printed-out papers, I think. Papers from PIs I'm familiar with are filed in a folder under the PI's name. Papers from unfamiliar groups, or papers on topics that I'm not very invested in, get filed in a folder with a topic name ("Poogly-plugs"). Before filing away the papers, however (and this is the only labor-intensive step), I import their citations into Endnote. If a paper is filed under the lead PI's name, no problem; if it's going to be filed under Poogly-plugs, then I type that in to one of the Endnote fields. When I'm trying to find a paper, I can just check Endnote to see if I have it, and if so where it's filed.
I'm happy with this set-up, because once every few months or so I have a day where I just can't motivate to do "real" work, so I grab my stack of accumulated unfiled papers, put them into Endnote, and file.
Dr. Hyde, in contrast, keeps an extensive archive of PDFs on his laptop. He doesn't have a good search solution (but he has a waaay better memory than I do....). I'm thinking about whether it'd be valuable to do something like that, for better browsing/indexing/linking/brainstorming purposes. Any thoughts?
15 years ago
13 comments:
I keep em on my computer... I use the following system (Last Name of first author, Journal (abbreviated, of course), Volume, Year of Pub). Then I have them in folders by subject- or if I am working on a particular project I have a big folder with all the papers that belong to what I'm working on. Of course if you are looking for something you have to be able to remember the last name of the first author...
I'm still not completely weaned off paper yet though!
I don't do any of this: no PDF archiving and no paper archiving. I remember everything I read. If I don't remember a detail, I remember enough to know of the existence of a paper addressing a certain issue, and can just pull the paper up on Medline. I don't enter citations into Endnote until I actually cite the paper in a manuscript or grant application.
I remember everything I read.
Jeez, that would work too. How? How many papers do you read? Do you spend a long time on each? Or do you just have crazy recall?
Of course, I might be especially spacy. Dr Hyde regularly ridicules me for not remembering conversations we've had.
DrdrA, yeah, the first name of the last author is my downfall. Even if I can remember the lab, I frequently can't remember the first author. And frankly, given how many junior people drop out of science, I don't care enough to put effort into that....
I keep them on my computer, but I then add the pdf link to my endnote citation (there's a space for both url and PDF link in the version I have); Endnote is great for being able to search everything--abstract, author, keywords--and then I just click to link to the correct PDF. The filing system I use for the pdf library is (last name first author, last name of last (or most famous) author, year, journal, abbreviated form of the title)
I print ones I'm going to read very thoroughly and actually use. They are filed by first author. But I always lose track of the hard copies, so even if I print one I'm likely to rediscover it as a pdf.
My pdfs get saved in one giant folder. I title them by first author and year and a few keywords that will trigger why the paper is important to me (rather than keywords they list). I can usually scroll through the folder to find things I want. It's not very efficient, but it's what I do.
I do something similar to Anonymous. I use Bookends. The nifty thing about that is that I can add keywords/concepts/results to the Notes Field and search that. Also, it automatically searches the abstract.
Oh and my hat is off to PP.
Jeez, that would work too. How? How many papers do you read? Do you spend a long time on each? Or do you just have crazy recall?
I read about a dozen per day. I spend about five minutes per paper. Yes, I have very good recall.
Maybe I'll write a blog post about how to effectively read a scientific paper in five minutes.
I use the Papers program. But not for searching, so far I mostly remember enough about each paper to find it again on the web.
In The Pipeline had a very thorough discussion of this a few months ago.
Thanks everyone for good suggestions and links!
PP, I for one would love some tips on increasing paper-reading-retention etc.
physioprof- i now officially hate you! I can't remember a damn thing. I like to think what I read forms nebulous mysterious connections in my head that generates innovative problem oriented thinking... I use Endnote, Papers, and keep pdfs mostly in one big file with LastNameFirstAuthor, PIName,Yr of Pub, sometimes journal or topic and whether it's a review. Some pdfs I keep duplicates of in special project related folders.
First off, nice blog DrJ and MrsH! Some very interesting reading, and it's been subscribed to. We need more science types blogging, most definitely!
As for pdfs, I do the linking of the pdf to the EndNote entry. That makes it a snap to find it when needed, as long as I can remember enough to get a small list via EndNote search.
pdfs are still named by my personal convention of LastNameFirstAuthor, ThreeLetterJournalAbbr.,Year, though once they're in EndNote, they have a number prefix added.
As for physical papers, they all get the EndNote record number written in red up at the top right. Then when I had a lot of printed papers, they were in hanging folders of 1-10, 11-20, etc. My system was so quick that a number of times my thesis advisor asked me for papers he knew I'd have.
But I'm throwing away anything that I have pdf for and haven't read recently. 2000+ references just took up too much space!
Another solution might be CiteULike.org, an online reference manager (simmilar to Connotea.org) which actually allows you to upload the pdf, and thus then access it from the web anywhere.
Endnote for me as well, attached to the reference. I haven't got them all in yet, but working on it....little by little.
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