Category Archives: Science

Science

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.

Using Google Notebook as a Lab Notebook

I love Moleskine notebooks, first of all. I have used them as lab notebooks for the last 2-3 years, and they are excellent all around. However, they suffer from the main drawbacks of hard copy anything:

  1. They only exist in one place at a time.
  2. They are not searchable in any modern sense of the word.
  3. Sometimes I can’t read my own writing [not a drawback for everyone].

Before Moleskines I kept my logs on our lab wiki, but that was a bit cumbersome.

Enter Google Notebook. I’ve written about other reasons to use Google Notebook before, and around the time I made that post I started using it as a lab notebook as well, but I wanted to give it a trial run for a couple of months before posting about it.

A couple of months have passed, and here I am. I’ve settled on the following format:

  1. One notebook per month: Each month, I create a new dedicated monthly notebook.
  2. Old notebooks are moved to Google Docs: It is possible to export a notebook directly to Google Docs. This is a more appropriate place for a long-term, large collection of documents, and it keeps the Notebook uncluttered.
  3. One entry per day: I started off with each logged item in its own entry. This became cumbersome. Now, I use one entry per day, with timestamps throughout the entry whenever a new item is added.

In contrast to the Moleskine, or other paper journals, this one is present everywhere that I have internet access, and is completely searchable with Google juice. I’ll post on it again after another few months’ use if I have any further insights or enlightening experiences.

Device handles chest compression part of CPR

Thanks to my grandma Tice for sending me this article:

The Lucas system runs on high-pressure air from either a compressed air tank or an air wall outlet in a hospital. The device is indicated for treating adults who have acute circulatory arrest – meaning they lack spontaneous breathing and pulse – as well as loss of consciousness.

Mechanical compression allows medical personnel to provide other therapies, the company said. The machine also should provide quality chest compressions for a longer period of time than a human can.

A 1995 study found that fatigue makes it difficult for even well-trained medical personnel to provide more than one minute’s worth of effective chest compressions, said Anne Devine, a Medtronic spokeswoman.

“Clearly these devices do much better compressions than humans do,” said Dr. Charles Lick, medical director of Allina Medical Transportation in Minneapolis.

Sounds kind of difficult to use, but apparently the EMTs like them enough that they’re putting them in ambulances.

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.