Category Archives: Other

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New Server

The blog has been moved to a new server. Things were a little wonky for a while, but now they seem okay. Let me know if you have any problems viewing the site / commenting / whatever.

Daily Work Log 2006-07-20

Today has been very odd. I just want to get out of here, eat dinner, have a drink, and watch a movie.

I can’t even begin to describe it all, partly for courtesy and political reasons.

Argh. I just hope I don’t get excessively rained on on the way home.

Research and Reference Management: Part The Second

Yesterday I posted a flow chart and a description of the first half of the process that it diagrams. Today, I’ll explain the more elaborate second half. First, for convenience, here’s the flowchart again:

The first part of the process gives me a prioritized list of articles to read. It helps, when I have time to read articles, if I can simply go to the list, get a few PDFs, print them, and read them. Therefore I typically go down the list and acquire PDFs for tens of articles in one go. That’s covered in the diagram. For each item on Cite-U-Like, there’s a link to PubMed. The important thing about that is that on PubMed, (while I’m on the University’s network) there are big icon-button things indicating whether I have full-text access to the article, and where. If I have full-text access, I follow the link and download the PDF. I then upload it to Cite-U-Like, which does three things for me.

  1. It keeps the file online for universal access (for me only)
  2. It renames the file to something sensible for me
  3. It puts the file in a nicely organized system with the rest of my article information

If, however, the article is not available to me in full-text (some institutions have more extensive access than others… *cough*), then I have to follow the “no” branch of the flow chart. First, I check the library’s online catalog to make sure that the library does not have the issue in question. They might have it. Ironically, they seem to have extremely obscure journals, but none of the really relevant ones. At least in my field. They also might have the article in J-STOR or Ovid or something like that. If so, then it’s time to descend into confusing multiple-electronic-database hell. I left that off the flowchart.

Anyway, so, the more likely case is that they don’t have it at all. That’s actually a relatively painless scenario, and it’s getting better. Most universities, including mine, have a nice online interface to request photocopies of articles via Inter-Library Loan (ILL). You request your article, and in a day to several days it arrives. Historically, the article would arrive in the form of a mailed or faxed photocopy. This was sometimes inconvenient. Why?

  1. You have to go pick up the article. If you’re doing this several times a week it can get pretty time consuming and annoying.
  2. The article is not digital. If you want to take the copy with you somewhere, you need to lug the dead trees. It is possible to scan the article using an auto-document feeder on a nice digital copy machine. This is yet another step, though.
  3. Sometimes they do a really bad job of copying
  4. Color figures usually become something between mostly useless and entirely useless after being xeroxed, especially if it’s not done with a careful eye for darkness settings.

The new thing is that most articles are delivered electronically. You get an email saying, “your article is in!”, you go to the ILL site and download however many arrived-articles have piled up, and you’re good to go. Of course, the issues of bad copying still apply, since nobody seems to use color scanning.

As you can see from the flowchart, no matter how the articles arrive, you can make them into PDFs somehow, and get them back into the Cite-U-Like library. From there, you can download the PDFs in order on the prioritized To Read list, and churn through them.

How to properly read and make use of the knowledge you gain from reading is worthy of several other blog posts. Questions?

Research and Reference Management: Part The First

To help me keep up with daily blogging, I’m going to try keeping the post window open all day so that I can add stuff easily.

Also, how do you like the new favicon? I thought it would be appropriate.

Today I’m spending a lot of time pulling references from various papers, adding them to my Cite-U-Like collection, trying to get the articles in PDF form if possible. Then, if Tulane doesn’t have the article I want via online access, I request it via inter-library loan.

I feel like I should have a flowchart for this. On my next break, it shall happen… (time passes)… Here’s the flowchart, and though it’s missing a few details, it’s mostly complete.

Here’s a little explanation. When I read an article, I circle the numbers of references that are attached to concepts I’m interested in. So, if the paper says, “widgets were frobbed using Magical Frabulation [12]” and I want to know more about Magical Frabulation, I circle [12] in red pen and continue reading. When I’m done reading the article, I go back to the article, find each circled number, and then circle the number on the actual reference in the reference section at the end. Then I use my hubmed search engine in Firefox to look up each reference. Usually I search using the last name of the first author and some pertinent words from the article’s title. If the first author has a last name like “Smith” or “Li” (do you know how many people named Li are on PubMed?) then I use a different author, if available.

I’m using the TabMix Plus extension, so every time I enter a Hubmed search a new tab automatically pops up. If the search worked, I carry on. If not, there’s a handy little search box at the top of the Hubmed results page that I use to try a different set of search terms. If it’s a medical article, I’ll eventually find it. If not, I have to look elsewhere and then my procedure has to be modified a lot. I left that out of the flowchart because it’s very case-specific.

Assuming it’s on Hubmed, I use my Cite-U-Like bookmarklet to post the item to my library. That’s the end of the first part of the process. I do that first part for each reference I want from the article. Depending on how I ranked those items in terms of how badly I want to read them, they will then show up in the proper order on my Cite-U-Like To Read list.