Category Archives: Software

Annotation of regulatory sequences is largely insufficient

Of a proven set of regulatory regions in zebrafish, computer programs find only between 29% and 61% of the true motifs. This does not come very much unexpected given the vast array of data shown by the Encode project. It even relates to the most basic question: What is a gene?

The more expert scientists become in molecular genetics, the less easy it is to be sure about what, if anything, a gene actually is.

iwith at least 5772 21U-RNAs? So – if I am sitting on the other side of the table when you are being examined don’t talk about junk DNA anymore, yea, yea.

Anonymizing genetic data

I have currently a paper under submission at the EJHG that covers ethical issues of genetic testing. One of the key messages is that genetic data are not anonymous if having simply stripped of names.
A story in a completely different field confirms my fears. According to a NYT article

Last October, Netflix, the online movie rental service, announced that it would award $1 million to the first person or team who can devise a system that is 10 percent more accurate than the company’s current system for recommending movies that customers would like.

but things turned worse by an article of Narayanan und Shmatikov Continue reading Anonymizing genetic data

Genome explained

You may want to read the full story at Public Rambling (fiction), the NYT article of Amy Harmon (fact) or the “Peepshow” article of Marco Evers (fact) and come back here afterwards.
The recent advances in genome sequencing (and typing) has left us with an enormous amount of data. Although technology has been available for a couple of years knowledge exploded only recently, where people now may decide to participate in a genome study or even have their genes tested on their own costs at DeCodeMe, 23andme, Navigenics or other personal genome service provider.
The main question is, what do these data really mean for us? Should we start an Open Source Project Genome Explained to collect the necessary annotation rules and provide a platform to apply these rules to local data? The data mode may be quite simple: Continue reading Genome explained

bibliographic.openoffice.org.call

Is there a working alternative to Endnote(R) or Reference Manager(R) for Open Office (noR)? The Bibliographic Project Homepage says that Continue reading bibliographic.openoffice.org.call

Prerelease: A universal study database engine

Last night I completed the prerelase of a new database engine that may be used both for online and offline collection of interview data and laboratory values. Continue reading Prerelease: A universal study database engine

Personal digital right management

is a serious issue as personal data in the internet grow exponentially. I have just recently completed a paper on informed consent in medical studies but think now it will not go far enough. In accordance with recent proposals at the Internet Governance Forum of the United Nations we might need a system that allows a personal digital right management where a server runs a checksum or does a reverse lookup before transmitting personal data – otherwise data tranfer should be aborted. See more at the EU funded project PRIME – I fear that people will no more participate in our studies if we can´t guarantee them confidentiality.

Dr. rer. photocop.

This is an old saying among medical students – you get your degree by copying a lot of papers.
When it comes to copy music I learned only recently that it makes a differences which software you are using to create a mp3 from your CD. Exact audio copy reads audio CDs almost perfectly while some other software does a jitter correction on scratched CDs. Differences can be really heard!
Back to photocopies – when I visited the largest medical library in Germany, the ZMB in Cologne, I was deeply impressed by all the students wearing headphones and sun glasses while copying pages hour by hour, an eldritch scenery, yea, yea.

GPS for biological pathways

After running a dual core CPU for two weeks I have a list here of all transcripts that are associated with the “ORMDL3” SNP gene cluster. Making sense from this list is a difficult task even with dozen of dedicated websites.
To get an overview of what is available I would start Continue reading GPS for biological pathways

Henryk Goldszmit (Janusz Korczak)

moblog – When being in Warsaw for the first time I wanted to honour Henryk Goldszmit / Janusz Korczak by visiting the orphanage. This was a home for Jewish children in the Jaktorowska (former Krochmalna) Street. Henryk, born 1878 or 1879, a physician, writer and outstanding pedagogue was the director of the orphanage since 1913. Continue reading Henryk Goldszmit (Janusz Korczak)

The first slide please

Thousands and millions of talks start with the “first slide please” although there is no “slide” at all. This post, however, is more about my problems to manage the 300 slide shows here while making a new one. I found some nice software, that can re-index my old PP slides, and let me drag and drop to a new slide show. Costs for Slide Executive are ~79€. Is there any alternative? Continue reading The first slide please

Increased stand by time

I could not find so much infomation out there about the HP Ipaq hw6515 power surge – my device runs on battery only a few hours if both GSM and GPS are being enabled. After several unsucessful attempts I found only two options to prolonge battery life – disabling both SD card slots and by CPU clocking down from ~300 to ~100 Mhz.