Jochen's Blog (page 2)

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26124 Advert: new lectureship in Leeds
2011-03-09

We are currently advertising a new lectureship in the statistics department of the University of Leeds. Thus, if you are a PostDoc and want to become a collegue of me, have a look at the job advert. The closing date for applications is 31st March 2011.

97570 Jvqplot version 0.1 released
2010-11-29

I am happy to announce the release of Jvqplot version 0.1.

Jvqplot is a data plotting program, resembling a simplified version of gnuplot. It is very simple to use, but it can only plot simple data files. The format and scaling of the plot is automatically chosen and cannot be changed. One of the main features of jvqplot is that the plot is automatically updated whenever the data in the input file changes. More information can be found on the Jvqplot homepage.

jvqplot version 0.1, 2010-11-29 (experimental version)

first public release

• archive: jvqplot-0.1.tar.gz (95KB)
  signature: jvqplot-0.1.tar.gz.asc
  sha1: 025b1e96eff5f8f57c8d78f30a612c15d36e6780
  md5: e6a19835d89be82d192c4821f164a849

This is the first public release of jvqplot. Any feedback about the program would be most welcome.

87757 TV licensing
2010-11-27

Since I don't watch TV programmes and also don't own a TV, I do not need a TV license. The TV licensing people seem to find this similarly difficult to believe than their German counterparts, so they keep hassling me about this.

Their latest letter seems to allow to declare online that I don't need a license. Unfortunatly, the web form quickly forces me to choose one of the following possibilities:

• Only watch pre-recorded programmes (DVDs/Videos)
• Only watch non live programmes via a Computer (e.g. Catch up services on iPlayer)
• Only watch non live programmes via a TV (e.g. Catch up services on iPlayer)
• Only use TV for games / consoles
• Covered by another licence
• I have no equipment

The last option seems like a possible choice for me, except for the fact that my computer probably qualifies as equipment. So which option am I meant to choose????

84419 What Every Computer Scientist Should Know About Floating-Point Arithmetic
2010-09-28

I just discovered the (1991) article What Every Computer Scientist Should Know About Floating-Point Arithmetic by David Goldberg. Very useful reading!

67118 Wisent version 0.6.1 released
2010-09-16

I am happy to announce the release of Wisent version 0.6.1. Wisent is a parser generator for Python. The new release fixes a problem (introduced in version 0.6) where comments and multi-line strings in grammar files were broken. You can download the program from the wisent homepage.

56133 birthday paradox
2010-09-15

I am slightly embarrassed by the fact that I've been caught out by the birthday paradox yesterday. The encounter went as follows:

While testing a new random number generator by analysing a list of 1000 generated standard normal distributed random numbers, I discovered that the list contained one of the numbers twice!!! This is suspicious, because this event has probability 0 in theory. After an (unsuccessful) hunt for bugs in my program, I finally found the following explanation.

The program prints the numbers using a C command like

printf("%f\n", normal(0, 1));

By default, the %f format string outputs numbers with a precision of six significant digits:

-0.641062
1.116142
1.417036
0.337435
-0.310383
...

Most of the numbers will lay between -2 and 2, i.e. they are concentrated in a set of about 4 million possible values. A quick check reveals that 1000 independent uniform draws out of a set of this size contains a number twice with a probability of more than 10%, and for the normal distribution the probability will be even higher because the numbers are more concentrated around 0. Thus, seeing a number twice is something which will actually happen from time to time and is no indication that the program is malfunctioning!

88724 scary phone message
2010-08-18

Just now, my (not very fancy) phone showed the following corrupted message to me:

I'm a bit at a loss about what is going on? If you have any idea, I would be happy to receive hints via email. Do I need to worry?

52851 using DSSP in the "bio3d" R package
2010-08-04

The program DSSP is used to determine the secondary structure of a protein, taking the three dimensional coordinates of its atoms as the input. Bio3d is a library for the statistical software package R which makes it easier to analyse protein structure; as part of this, bio3d contains an interface to DSSP (in the function dssp). Since I had a bit of trouble using this interface, here are some hints.

1. Get the DSSP program from the DSSP webpage. For academic use, the program is free of charge, but you need to fill in a license agreement.
2. Rename the executable to dssp (mine was called DSSP_MAC.EXE after I had downloaded it).
3. Move the file to the directory where it will live. For my system (and for the examples below) I chose /usr/local/bin/. The name of this directory is not allowed to contain white space.
4. Call the dssp function with this directory as the exepath argument. The value of the exepath argument must end in / (on Linux/Unix/MacOS) or \ (on Microsoft Windows). Also note that every \ in an R string constant needs to be doubled, e.g. on Microsoft Windows you will probably need to write something like exepath="C:\\path\\to\\file\\".

Example. In R one can now use the following commands.

library("bio3d")
pdb <- read.pdb("12as")
x <- dssp(pdb, exepath="/usr/local/bin/")

Then the secondary structure information of the protein 12AS can be accessed as follows:

> x$helix
$start
  1   2   3   4   5   6   7   8   9   1   2 
  5  76 130 170 182 258 277 297 320 271 310 

$end
  1   2   3   4   5   6   7   8   9   1   2 
 27  83 155 176 193 268 283 305 325 275 312 

$length
 1  2  3  4  5  6  7  8  9  1  2 
23  8 26  7 12 11  7  9  6  5  3 

$chain
 [1] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A"

This tells us that the first helix reaches from residue 5 to residue 27 (both inclusive).

73630 cereal grains
2010-08-03

I learned about the different kinds of grains long ago, when I was in primary school. Since then I have somehow managed to confuse myself about which grain is which. Here's to unconfusion! (All information and pictures are from Wikipedia; follow the links for details.)

name	picture	comments
wheat / Weizen (Triticum aestivum, Triticum durum, etc.)		Used for bread, flour, couscous, beer, biofuel, … Needs good soil and climate, several species of wheat are used, main source of vegetable protein in human food.
barley / Gerste (Hordeum vulgare)		Used for beer, whisky, animal feeding, … One of the first cultivated crops (together with einkorn and emmer).
oat / Hafer (Avena sativa)		Used for animal feeding (e.g. horses), oat flakes, porridge, … Can be grown in regions with relatively cold, wet summers.
rye / Roggen (Secale cereale)		Used for bread, animal feeding, … Can grow on relatively poor soil and in colder climates.

33420 new puzzle game
2010-06-27

In the last days I have finished my first ever browser-based game: a puzzle, based on the classical fifteen puzzle. Cou can play the game here and download the source code from the program's homepage.

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