Just reveived an email from the creators of the Genetic Association Database (GAD)
… Your published genetic association study has been included in the recent update of the NIH based, Genetic Association Database (GAD), the database of human genetic association studies. Continue reading Genome Browser now with GADview track
… permanently leading to errors – the plus / minus strand orientation and the consecutive sequence / allele designation of SNPs. Only recently I came across a fancy way how to define strand direction – from a tech note Continue reading Orientation of genomic sequence and SNP allele designation
How many times did you hear that from an editor? At least I hear it 5 times every year … But have you ever heard of journal saying this is paper better suited to a more general journal? Never! So, this is a never ending loop, yea, yea.
Occasionally I see high R^2 values even between linkage disequilibrium blocks. The following plot was obtained from the German asthma family study; basically a haploview screenshot rescaled and inverted before using the Photoshop polar filter. Continue reading Trans-border LD?
Following the protestantic view of science here are some thoughts that I found in the new book by Benedetto XVI aka Joseph Ratzinger “Jesus von Nazareth”. Rationality as divine gift? Yes, Benedict follows the Historical Critical Method but wants to reconcile it with revelation that is not accessible to logical arguments. While it is not a book on science Continue reading A catholic view of science
Here is the announcement of an allergy meeting in London (where I will be too :-). Continue reading Allergy School
I am not sure if my count of sequenced individuals is correct. While the Human Genome Project and Celera used a DNA mix for their draft version of the human genome, the next genomes were provided by Watson and Venter. Numer 4 to 12 were Continue reading Women explained
c’t 10.2008:82-89 has a nice article about open peer review “Die Weisheit der Massen” summarizing the current peer review process – the top line of the cartoon below. Following submission of a paper, it is initially screened for some formal requirements before being submitted to anonymous peer review and finally being published. Anonymous peer review lasts between 2 months and 2 years (!) and is abbreviated so far only by one biomedical journal Continue reading Open peer review – publish first, review later
Over the years I have collected a lot of curious hypotheses how allergy develops. Only recently I ended this list as it became rather long – and to be polite – rather useless. Sorry, less polite – but nonsense at its best Continue reading Rough and tumble science
Looking at the log file I found that an anonymous visitor was looking for “Jim’s DNA data” here. I thought of James Watson first. Obviously, however, the anonymous visitor was looking for something different: Continue reading Your DNA data here
During my recent trip to London, I could get a brief glimpse into the 1932 book “Vitamin D” by Reed, Struck and Steck. As this volume is not available in a German library and as it was not allowed by the British library to travel, I took now the lengthy procedures of registering, waiting in the queue, before searching this book for any allergy related items.
It seemed to be worthwile, although with some unexpected results: Continue reading More retro vitamin D
Tip 1: Avoid loops.
They are generally slow – use a function instead. Even with the need of variable and fixed columns in a loop, a function may be constructed like
apply(data,2,function(col2){table(col1,col2)
Tip 2: Always show current state.
Include options(warn=1) and show current state with cat(“message\n”);flush.console();
Tip 3: Avoid merging steps.
Use instead datasets in same order and with the same subset of the larger table before updating anew column with data from the second table.
It might be fun to read here on a genetics board about DNA (Direct Note Access) which is a technology implemented in Melodyne that can extract notes from polyphonic music.
So far, it does not use a library of musical instruments according Peter Neubäcker, head of development, in an interview published in c’t 8/2008, p 34. It separates “musical content” defined by periodicity, similar overtones and meaningful musical distance like halftones. Although that’s something bioinformatics is trying for some while for DNA (desoxyribonucleic acid), I wonder if the decomposition concept in DNA would works also for DNA, yea, yea.
This morning when leaving the Munich underground, I could hear Ivan – the best accordion player in the world. There are numerous videos at YouTube, so listen if you like Continue reading Ivan Hajek – there is no better accordion player
The BBC headline yesterday is close to the famous quote of Neil Amstrongs’ with reporting the United States blocking now genetic discrimination.
Or as Kennedy put it forward “the first new civil rights bill of the new century”. Unfortunately, we are lagging behind in Europe. My recent initiative to promote such a legislative in Germany was futile; the most recent goverment proposal only earned a lot of criticism.