Category Archives: Science

Science

LaTeX Word Count

I’m working on my graduate thesis in the LaTeX document mark-up format, and trying to apply Anthony Burgess’ Martini Method. Basically, set a certain desired word count and let yourself relax after you’ve achieved that word count every day. I started off pretty well with this method, but the next day my wife Amanda went into labor, and my productivity has basically been a train wreck ever since.

I’m getting back on the horse.

Anyway, it’s a little tricky to apply the Martini Method when using LaTeX — as a markup language a bit like HTML, it’s full of special words, symbols, characters and whatnot that are not actually part of what you’re writing. A simple Emacs word count will not do the trick. Much as I’d love to count all of those extra words, the point here is to produce a certain volume of output and that would miss the point. Plus, it’s dishonest. There exists a PERL script that will parse LaTeX and count the non-special words. However, someone’s gone even a step further and made a nice web interface for it, with color coding and everything. That interface is here, apparently hosted by one Einar Andreas Rødland in Norway.

So far, it’s working quite well for me. Unfortunately, it just informed me that I’m not quite to my desired word count yet. More writing!

Passed my GBO

I had to take a “Graduate Board Oral Examination” — typically called a GBO and synonymous with “qualifier” — in order to be able to get a Hopkins PhD. It’s necessary and not sufficient, of course, as I still need to do a thesis defense. I was fairly worried about it, and with good reason, but things went very well and now I’m one step closer to graduation.

Now all that’s between me and the PhD are a few simulations and a lot of writing. I think I’m going to employ Anthony Burgess’ Martini Method. 1000 words per day, after which I can have a martini, relax, etc.

There’s also the small issue of my baby arriving soon, which will certainly complicate matters.

Hiatus

After a valiant attempt to keep up a regular posting schedule starting in January and lasting until about March, this blog has been on an unofficial hiatus for a while. I’m making it official today.

I am a new (as in recent) homeowner, I’m trying to graduate, I moved across the country, and I have a baby arriving in two months. This morning I had an epiphany — even though I try to keep anything that’s not immediately important in my Someday/Maybe category (in GTD), all kinds of things had crept in to my active system that were not pressing. A number of those things were blog post topics for VirtuallyShocking. After doing an aggressive move of many items to the Someday category, my active, actionable items dropped from about 80 to 35, and I can see now looking at the list that it will be much easier to retain my focus.

I’ve never been a terribly prolific blogger — this is mostly a diary blog, despite my best intentions to the contrary. In that vein, it will continue. I’ll probably keep up with the hearty Friday posts and occasional updates. Part of the reason for this is that most of the cardiac electrophysiology stuff that I’ve really wanted to blog about, I can’t, because the stuff I’m excited about is stuff I’m working on. That stuff generally needs to remain private until the related papers are published, at which point I’m generally already more excited about the next thing, and not interested in talking about the older stuff.

Hopefully once I graduate that will start to change, and I can build this blog the way I’ve really wanted to.

Hearty Friday – Ott et al.

I have a special Hearty Friday for you today. Recently, there was a very cool paper published in Nature by some people at the University of Minnesota, Harvard, and several other institutions.

The HubMed page is here, the Nature Medicine page is here.

I plan to review this article at some point, but for now, here’s a picture of their recellularized scaffold. That is, they took an animal heart, washed all of the cells out, leaving the fibrous scaffold, and put cells back in, letting them grow back into a beating “heart”. This is snapped from Figure 4 of their paper.