Mailund on the Internet

The last two weeks I’ve been busy with writing a grant proposal, so I haven’t had much time to read (much less write) blogs, but here’s a list of the posts that I did have time to read and enjoy…

Biology

• A flurry of red and green (Byte size biology)

Human ancestry

• Australian Aborigines arrived via South Asia (Gene Expression)
• Real stories of the Neandertal CSI (John Hawks)

Research Life

• Igor – a Google Wave robot to manage your references (Nascent)
• PLoS Journals – measuring impact where it matters (PLoS)
  • A step in the right direction. PLoS makes a move (bbgm)
• How many hours do people really work? (Sciencewomen)
• We are not responsible for what happens next (Bioephemera)
• Tempering justice with mercy: the question of youthful offenders in the tribe of science (Adventures in ethics and science)
• How would you like some posturing Congress Critter to de-fund your grant? (DrugMonkey)

Software

• The Canonical model for scientific software (bbgm)
• Is Linux currently at a fundamental disadvantage owing to how computers are set up? (Gred Laden)

Space exploration

• Moon astronauts urge Mars mission (BBC)
• A giant leap to nowhere (NYTimes)
• A space program for the rest of us (The new Atlantis)

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208-205=+3

Back in 2003 I wrote a small parser for the Newick tree format.  It is pretty straightforward Python code, and basically just something I hacked up because I needed to manipulate some trees for a project.

Figuring that others might also find it useful I put it on my webpage and that’s about it for the story of my Newick parser. I’ve used it in a few other projects, but haven’t really developed it further from the initial code, and haven’t really received much feedback on it.

Except for this weekend where I got three emails about it.  I might have received one email a year until now.

It was a few bug reports and some questions, and because of the bug reports I’ve now made a new release, version 1.3.

I also have a Newick parser for C++.  Actually, I have more than one, since there are two different parsers in QDist and SplitDist, but the one I have in mind is more stand-alone and can probably be used by others.

It is a recursive decent parser I wrote in Boost.Spirit as an exercise to learn the Spirit language.

I think I will clean it up a bit and put it up on the web…

According to this press release, some people at Harvard Medical School have developed a new programming language for biological modelling.  I guess protein modelling from the description, but I could be wrong.

“Through incorporating principles of engineering, we’ve developed a language that can describe biology in the same way a biologist would,” says Jeremy Gunawardena, director of the Virtual Cell Program in Harvard Medical School’s department of systems biology. “The potential here is enormous. This opens the door to actually performing discovery science, to look at things like drug interactions, right on the computer.”

I’m not sure how much of a domain specific or how much of a general purpose programming language it is.  They are comparing it with LISP, so maybe it is a domain specific language with some meta-programming features?

I haven’t been able to find the paper yet — of course it isn’t published until today and there might not be any preprints online — but I’m curious about this…

My friends at CLC Bio has just released their Genomics Workbench.  When I talked to them last Friday, I couldn’t quite figure out what the marked for this software is, but Next Generation Sequencing is a hot topic right now, so there probably is one.

Anyway, I wish them luck with it!

Wednesday this week I’m giving a talk at the Danish Society for Computer Science. I was asked to give the keynote talk at this years general assembly before they hand out this year’s Best Thesis Award.

I’m tired of talking about my main project — association mapping — so I decided to give a talk on our CoalHMM work (although I am only working on that a small percentage of my time).

The slides file is too big to upload to slideshare, but if my flash hack works you should see them below:

You can also get it as a PDF file, a PowerPoint file or a Keynote file, if you want.

The last couple of presentations I’ve made I have been using the Keynote program on my Mac. I’m really happy with the program. It makes it very easy to put together pretty presentations (if I say so myself) with very little work. Especially its handling of graphics impresses me. Compared to using OpenOffice, as I usually did before getting the Mac, there’s essentially no work involved in including graphics. Automatic masking and alpha channels beats modifying images in Gimp any day!

I couldn’t really figure out how to put presentations on my homepage, though. Keynote files are really directories, so you cannot just copy them to the homepage directory. I found out, though, that if a Mac downloads a zip’ed Keynote file it will just open it in Keynote, so I guess that is the way to do that.