Category Archives: Software

WikiPathways

As somebody who is dealing most time with large datasets I always arrive at genes and proteins that I do not know. Using Biocarta, Keggs and other services in the past, I find the new WikiPathways exciting and hope that it will grow over the years. A companion paper in PLoS biology describes its roots in GenMAPP and the current work of the authors on bots that identifiy inconsistencies but also pick up loose ends. Hopefully I will find some time to work a bit on nuclear receptors, yea, yea.

CNV (not London) calling

Having been asked now by several people, I am compiling here a list of programs can be used for CNV calling. Continue reading CNV (not London) calling

Webcam based laser point tracking

If you do have the same problem like me – operating a computer, pointing towards a wall and looking at the same time at an audience is somewhat odd – here may be a solution for you.

Initially found this at a blog with some java source code.
Another video example is

with abandonded C# code that compiled nicely on my mac (laserinteraction). Experiments are ongoing…

PDF Pubmed Finder

As announced earlier this week, here is a first version of the PDF Pubmed Finder.The Finder helps to identify an unknown paper within seconds and rename it within milliseconds. Although the Finder consists of a single page only it uses several areas to update the data. I have written the code for my local installation but you may try it also online with your own PDFs either by uploading them with the available form or by appending the PDF URL to the Finder address http://wjst.de/pubmed/finder.php?http://medicine.plosjournals.org/test.pdf
The last method is certainly better as it can be used within a scripting environment; note that my domain may not retrieve a PDFs that you can see at your local computer. PDFs also need to have some inline text (run an OCR on scans before submitting them).

zotero_c2.png
Here are some usage instructions: After selecting any article on the left (1.), clicking on relevant keywords (2., 3.) will lead to an immediate Pubmed search (4). Finish by clicking on “rename” or “Pubmed/Zotero” import of the correct reference. If your search doesn’t retrieve any useful hits, keywords will be automatically reset.
What I would like to know all from the AJAX experts who can inspect the sourcecode: I ran into deep problems described earlier with the prototype oncomplete function used in the links of the div2 container. They are checking how the div4 container was being updated. As you see it works, but I failed to clean up the code by having only one Javascript function in the beginning of the page with the div2 links calling this function. Your help would be greatly appreciated.

Genome Browser now with GADview track

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

Orientation of genomic sequence and SNP allele designation

… 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

Open peer review – publish first, review later

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

DNA for DNA

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.

Our lives are unrepeatable experiments lacking a control

a prosaic quotation from the recent Nature correspondence section that highlights why genetics has been leading us into nowhere.

Our lives are unrepeatble experiments lacking a control. Myriad external factors interact with genetic and epigenetic factors and with chance to determine whether we are well or ill, smart or dull, successes or failures.

Yea, yea.

How to impute marker genotypes

I am currently playing with MACH and SNPMStat to impute marker based on public datasets. I do not have any opinion about the usefulness of this approach – largely due to the fact that ~10% of my allele coding is different to the public hapmap data. Continue reading How to impute marker genotypes

More Zotero support

Welcome Just Science Participant! Here is an extra primer how to store your references from the scientific papers that you are reading. In 1983 I was writing on cards, moved to a simple 4-column-database in 1989, used Endnote in 2005 and eventually moved to Zotero in 2007. Zotero is an open source database that sits as a plugin in your Firefox browser [download link]. The neat thing Continue reading More Zotero support