Category Archives: Tools of the Trade

Tools of the Trade

PubCasts and SciVee

Have you noticed that everything is named in CamelCase these days? Anyway…

I’ve had a couple of conversations with Dr. Rachel Karchin here at the ICM regarding Open Access scientific publishing, and PLoS specifically. Last week, she forwarded an email to me regarding PubCasts on SciVee. (Example here.)

A “PubCast” is basically the same thing as a “SlideCast“. (Have you noticed that everything is named with “Cast” at the end lately, all spawned from the term “Broadcast” and made popular by “PodCast”?) Let’s start with a SlideCast. The idea with a SlideCast is that presentations are not composed merely of speaking or merely of slides. Many people make their presentations in such a way that the slides stand on their own, but these are typically awful presentations. They’re just slide-formatted outline notes. A good presentation requires the visuals and spoken commentary. In a SlideCast, slides with their various animations and transitions are shown with an audio narration by the presenter. PubCasts go one step further and actually include video of the presenter speaking along with the slides. They also preferably include the paper. I think the video is probably not necessary, unless it’s video of the person presenting in front of the actual slides, but that requires green screening or extremely high quality video (for the slides to be readable), both not worth the hassle.

On the whole, I think PubCasts are an excellent idea. A proper scientific presentation should get the audience engaged by getting them emotionally involved, making them see why they should be interested, while a paper gives all of the gory details. In this way, you get both together. How often do you have the paper handy to follow along when watching a scientific presentation? In my experience, pretty much never. People usually present the stuff they’re working on, not the stuff they’ve published (background excepted).

Unfortunately, I don’t have any true Open Access papers yet. My paper that’s supposed to come out next month will not be Open Access, as the fee from the publisher for it was outrageous, and I couldn’t really justify it to my advisor. Nonetheless, I already have a slide deck put together for the paper, and have presented it, so in the near future I’m planning to do a SlideCast of it and post it here on the blog.

PHPMyGTD “bug free” (ha!)

My pet project is coming along well. Tonight I made a bunch of UI improvements, and eliminated every single bug from my to-fix list.

There are still some more UI things that really should be fixed (like chiding the user for incorrect date input rather than simply adding an item with no due date), but I think I’ll probably have a beta release to post as a downloadable package on SourceForge soon.

Along with that will come a document page showing and explaining the UI.

GraphClick for Digitizing

As a scientist, I often read others’ scientific writing and work. Typically such written work includes plots and graphs — much more efficient and insightful ways of showing data than extensive tables. However, sometimes it’s important to extract more exact values from such plots. Traditionally this was done with a digitizer, a fancy mouse that worked on a special pad. You’d place a printed figure on the pad, and use the crosshairs on the mouse to pick out points. Then, using some scaling calibration, you’d derive values from points on the graph.

GraphClick does the same thing, but with digital figures. Typically, I use it with figures snapped directly from PDFs of papers, though it would work just as well with figures scanned from hard copies. Rather than explain more about how it works, I’ll direct you to the screencasted tour.

GraphiClick is a commercial, closed-source application, but it is available for free use with a limited feature set. I never found in using it that I needed any of the more advanced features. If you ever need to pull data from figures, and you’re a mac user, I highly recommend you try it out. I used it extensively for my soon-to-be-published paper, and I couldn’t have asked for anything better.

PublicationsList.org

There’s a relatively new service available on the interwebs at PublicationsList.org. It’s basically Cite-U-Like specifically tailored for on person’s papers — your own.

You can import common bibliographic formats such as RefWorks and Bibtex, and for those in the medical field, directly search for and add papers from PubMed. It then appears (though I haven’t investigated thoroughly) that you can add various details including PDFs of or links to your papers. I already sort of do this on my publications page, but this has a slick interface and is independent of my web server.

Unfortunately, they don’t seem to want you to embed the nice resulting list directly in your web page. I’m sure there are ways around this with some clever PHP, but that would probably violate the terms of use. They do give you a nice button though:


Publications list

Similar to .

Their business model seems to be based on getting whole organizations to subscribe to their service, but individual accounts are free. Might be worth looking into if you’ve been meaning to put your list of publications online, but have been too lazy or whatever to type them all out somewhere.

ADDENDUM 2007-09-29 @ 17:43 EDT: Apparently they allow embedding if you are a paid member.

Finding Biomedical Citations with HubMed

Have you ever read a paper or two, found a bunch of interesting references, but avoided looking them up because it would be so arduous?

Procrastinate no more — you can use HubMed‘s Citation Finder! Just copy your references directly from the source paper in a PDF reader, and paste them into the big text box. HubMed will then find the citations, allowing you to correct those that it couldn’t find.

Ingenious.