An excellent new review summarizes our current knowledge about telomeres – the complicated chromosome end machinery that is necessary to prevent unwanted repair while allowing to track for the number of replications. Think of it like a source code control system as CVS, the Concurrent Version System. During a recent research project on life cycle of single point mutations / SNPs I realized Continue reading Living on borrowed time
I had the chance to install now the new PLINK GWAS software for a further analysis of recently published ORMDL3 asthma data. It seems that PLINK is some software that I was looking for a long time (paper link|download link). There are great and foolproof functions to check the validity of your data. I discovered for example unnoticed stratification in the German case-control sample by first and second component of the MDS analysis Continue reading Blink Plink
New work in mice published in nature neuroscience now show that ordinary fever is caused by prostaglandin E2 stimulation of EP3 prostaglandin receptors in the median preoptic nucleus of mice. EP4 seem to mediate hypothermic response, leaves you to choose not only ambiyour desired body temperature
In a previous post we have create calendar snippets in ics format. PHPicalendar is the ultimate solution to stitch these calendar snippets together to a workgroup view.
I am using the built-in RSS feed to be noticed about any forthcoming events that are not sitting in my own calendar.
There is only one drawback: phpicalendar doesn’t offer any possibility to import back any new meeting into Sunbird or Outlook. By using the following patch of events.php it may, however, send you back an .ics file (that can opens Sunbird automatically if configured correctly) by just clicking on any new event.
events.php
|wj_events.txt|
If your calendar ics are really up to date, you may want to change $actual_calname in ical_parser.php to
$actual_calname = getCalendarName($filename) . ‘ (-‘ . round((time() – filemtime($filename) )/100000) . ‘ days old)’;
There is a nice online example of four datasets that show exactly the same variable mean AND Pearson R^2 although they look quite different!
I show here an alternative R solution for the correlation ratio eta that may help if you are dealing with such data.
anscombe.R
|wj_anscombe.R|
The R Munich user group likes Sweave. Here are 3 screenshots how to create a seamless R + Open Office integration (which works also for Word documents if you have installed the ODF converter plugin). First create your document
sweave.R
|wj_sweave.R|
the document
save it, open R and execute
Your document will then look like
I confess: I have clicked here
Stem cell researchers now believe that the human ES cell line SCNT-hES-1 (you may renember Hwang who claimed having first cloned a human by somatic cell nuclear transfer) is derived by parthogenesis – the result of a dividing human oocyte.
They test the origin of the Hwang cells by genome-wide SNP analysis as the initial DNA fingerprint was doubtful Continue reading Human parthogenesis
Doping rules are sometimes hard to understand. Sleeping in a low pressure chamber and training at high altitudes is allowed but taking epo is not – although net effects may be the same.
This might be a reason why some athletes are now trying to mimick more closely biology. Repoxygen is a viral vector known for some time that includes the human epo gene under control of a hypoxia control element. Clearly this drug has the potential to be used for doping (“Outlaw DNA“). Continue reading Detecting repoxygen infection
I currently hunting some transcripts of unknown function (see below), possibly a RNA gene? while it is difficult to locate any good annotation server. So far I tried RNAz based on a PNAS 2005 paper – another one was RNA Genie. Next step will be the new Gingeras paper that describes even a new class of RNA genes. Finally this may not even be a RNA at all but an alternative leading exon … Continue reading RNA genes – dark matter of human biology?
Nature genetics asked about 30 eminent scientists “What would you do if it became possibe to sequence the human genome for only $1,000?”. Unfortunately, this initiative has been launched 4 weeks too early as I believe some may have responded differentially if they could have a chance to read the ENCODE papers… The majority of scientists seems to follow the idea of Continue reading Question of the year in genetics
Manipulating large SNP datasets has always been a hassle, a lot of cut & paste, quick & dirty database resorts and no documentation after all. Only by the last week, I learned form the ENCODE papers that there is now a web service that helps with all kind of these tasks. Check out Galaxy — a “must have”.
When starting again analysis of pooled DNA samples – this time on the Affymetrix platform – I discovered not only the much improved “Genotyping Console” but also that my earlier Genepool binaries do not work anymore under VMWARE/Ubuntu. I therefore tried Continue reading My linux box
Do you wonder what QQ means? These are quantile – quantile plots that rank observed test statistics against expected test statistics. They allow a visual inspection of overdispersion due to population substructure or other sources of biases.
QQ plots have been recommended earlier, are now frequently used and available in the snpMatrix R package. Yea, yea.
