Genetics

Outlook calendar export

It should be quite easy to export Outlook appointments into .ics format and let third party applications like phpicalendar stitch these snippets together into a coherent view. Unfortunately older Outlook versions are not supporting ics export. After several frustrating attempts (installing VB macros that are buggy and software like freemical that misses important fields) I finally wrote my own exporter that includes also a category filter as otherwise too may entries will have to be parsed by phpicalendar.

ol2ics.zip includes the source perl script including a compiled windows version.
|wj_olics.txt|

The ics file may then be uploaded to the phpicalendar directory using a wput call like
wput –reupload my.ics ftp://name:password@domain.de/calendar/my.ics


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Joke

Punch line

I have seen the first user looking here for the BMJ Christmas edition already 2 weeks ago — clearly the annual highlight in the biomedical world since 2000. But only today, the 2007 issue is being online. As a former recumbent owner, I can assure you that Professor Shuster’s observation is correct. Even with my folding bike in the Munich S-Bahn I get many responses from the public, usually technical questions by men but also price inquiries by women. Continue reading Punch line →


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Allergy

Forgotten papers: Allergy origins in the gut

Instead of highlighting the best paper in 2007, I decided to nominate now the most under valued paper in 2007. There are so many interesting (and probably highly important) studies that do not get enough initial attention and consecutively fail to enter the high citation track. Here is one of these papers that is as interesting as on the day of publication: Continue reading Forgotten papers: Allergy origins in the gut →


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Software

Do ScribeFire and Zotero work together?

— an important question for a science blogger. The answer is yes, at least in principle, as you can see from my screenshot: I am able to drag and drop a reference from the Zotero list view into the Scribefire edit pane. As the reference appears there in full text only, I have already submitted a support request at the Scribefire site as. I think we need to implement DOI support and I will look into the possibility to write a Zotero plugin. A quick fix to reformat the dropped reference would probably be a simple bookmarklet.
BTW The Endnote import into Zotero works best with the “Refman” option on the UPPER RIGHT BAR in Endnote selected before starting the text export. The resulting text file then can be flawless imported in Zotero if it contains less than 100 or 200 references.

scribezotero.png


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Philosophy

No scientist is always a scientist

Today I watched the full length video of the Nobel prize ceremony last week. I had to think of Stefan Zweig saying in “Sternstunden der Menschlichkeit” (my own translation)

No artist is always an artist during 24 hours of daily life; everything that is important, ever lasting and successful, happens within a few and rare moments.

in other words Csikszentmihalyi’s “flow” that we are always chasing, surfing the ultimate wave, yea, yea.
img003050.jpg


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Genetics, Joke

Why men die earlier

It took me nearly one hour to locate also this series of pictures on the net after having seen them recently in the talk of a Spanish colleague.
Yes, there are also more serious comments for example in the Behavioural Issues Blog Continue reading Why men die earlier →


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Philosophy, Software

Research not re-search

Zotero is a browser plugin that I am currently exploring as it can recognize PUBMED or PLoS entries and knows about Endnote/Refer/BibX export in UTF-8 format. The Open Office 2.1 insert reference macro produces a runtime error here and importing 100 references freezes my computer for about 5 minutes. Nevertheless Zotero follows a promising concept and holds much premises for the future; just discovered that data are stored in “…\zotero\zotero.sqlite”, great! one of the best available databases. This is the reason why I will
Support Zotero with WordPress
yea, yea.

Addendum 1

As there is no central Zotero server, I wonder how I could access my local installation from different sites. The recommended portable Firefox is not really an universal solution. As with other open source databases, surrounding code of SQLITE is getting commercialized but there seems to be a free? sqlite server for download.

Addendum 2

This is a more philosophical remark on science publication: With a technical sound solution for online referencing I expect that science blogs will get more influence while printed papers will loose their importance. Post publication peer review (attached comments) is certainly as good as pre publication peer review (that kills many new ideas, always delays publication and costs a lot of money better spent for research). You can cite me for that idea ;-)


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Allergy, Vitamins

Hans Selye: Ancestor of the allergy vitamin hypothesis

1 Comment

I spent a lot of time in libraries verifying bibliographic lists as I expected that somebody else could have had the idea of allergy induction by vitamin D before — in particular when being closer to the introduction of vitamin D supplements. Fortunately Science Magazine now offers a fulltext search of their archives (what is currently not possible with old Nature volumes). I could locate about 70% of the computer hits when searching manually the Science index for vitamin and hayfever. The loss of about one third could be mainly attributed to the fact that extra supplement pages have only occasionally preserved in the libraries that I have visited for this project (Marburg, Berlin, München STABI + TUM, Garching). Text recognition is also limited, so my results may be preliminary.

What I found this afternoon in the library at TUM Garching Continue reading Hans Selye: Ancestor of the allergy vitamin hypothesis →


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Genetics, 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.


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Genetics, Software

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 →


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Joke

First we take Manhattan

They sentenced me to twenty years of boredom
For trying to change the system from within
I’m coming now, I’m coming to reward them
First we take Manhattan, then we take Berlin
I’m guided by a signal in the heavens
I’m guided by this birthmark on my skin
I’m guided by the beauty of our weapons
First we take Manhattan, then we take Berlin…
(thanks to Leonard Cohen for a true science motto


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Genetics, Software

Genome explained

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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 →


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