Mailund on the Internet

Genetics

• “Filled up with other books” (John Hawks)
• Scientists launch effort to sequence the DNA of 10,000 vertebrates (ScienceDaily)
• The genomic ark: 10,000 vertebrate genomes (Byte size biology)
• Complete Genomics produces a cheap — well, $5,000 — human genome (Ars Technica)
• First ever association study using whole genome sequences (Genetic future)

HPC

• High-performance computing technologies for genomics (Next generation sequencing)
• Setting up Xgrid (MacResearch)

Programming

• Complex networks in R (Michael Knudsen)
• Floating-point errors, explained (Revolutions)
• Python in the scientific world (Neopythonic)
• Google opens up its JavaScript development toolbox to all (Ars Technica)

Science life

• What keeps me up at night (Uncertain principles)
• Distributed science, part 2 (Common knowledge)

Misc

• The Ares I-X rocket special (Starts with a bang)
• Anime film characters: do we perceive the intended race, or our own? (Cognitive Daily)
• Preserving our digital pre-history (Coding horror)
• Native language shapes the melody of newborn baby’s cry (Not exactly rocket science)

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Another thing we can celebrate today is Carl Sagan’s birthday. Carl Sagan (1934-1996) most famous I guess for his popular science writing and the Cosmos tv-show back in the eighties.  I’ve recently been watching a bunch of the episodes and although they are pretty old by now, they are still very much worth watching.

More at Primate Diary.

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That’s Nov 9, not Sep 11, for you guys out there who use the weird month/day/year notation…

There is nothing to celebrate Sep 11, but Nov 9 is a day for celebration, and today we celebrate the 20 year anniversary of the fall of the Berlin Wall which is as good a date as any for celebrating the end of the Cold War.

I was in Berlin a few weeks after the fall of the wall myself. That was on a trip that was planned before the fall of the wall, so it was pure luck that I experienced this historical event first hand.

It is hard today to imagine how east and west Europe was separated and practically two different worlds. Today, I have many friends from eastern Europe and the former USSR; that would not have been possible 20 years ago.  We have students here at BiRC and at AU in general from the other side of the iron curtain.  That would not have been possible 20 years ago.

Today is truly a day for celebration!

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Mohamed El Naschie is suing Nature ’cause they accused him of abusing editor privileges (pdf) to self-publish poor quality papers.

Well, if the papers were reviewed by peers, it shouldn’t be a problem to prove that, and the the case has merits, but otherwise there really isn’t any case at all.

The number of self-publications in the journal, though, would make me bet that Nature is right on this one, though…

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Once again I find myself writing lecture notes for my programming class Applied Programming.

It is a lot of work, and I really would prefer not doing it and using a text book instead, but all the text books I have seen for Python programming falls in one of two categories: Either they assume that the reader is a moron who has to have everything explained in every single little details over close to one thousand pages, or they assume that the reader already knows how to program and just needs a quick introduction to Python.

Neither really fits my purposes.

I have seven weeks to teach basic script programming, so I only want to cover the bits really essential for that, and since I teach mainly biology and medical students I can safely assume that this is the first time my students are exposed to any kind of computer programming.

It is the second time I teach the class, and last year I tried using a text book supplemented with lecture slides, but that didn’t really work so well, so this year I am going to write enough lecture notes to cover the material I need.

I had to write my own lecture notes in previous programming classes as well, but those classes was for people familiar with the basics of programming and Python who just needed to know a little extra stuff useful in bioinformatics, so those were completely different notes and I cannot reuse any of it this time.

I plan to spend one day a week on lecture notes this time around.  I don’t have time for more.  We will see how that goes, and how much I need to add on top of it next year, where I can take the next iteration over the notes.

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