Do ScribeFire and Zotero work together?

19.12.2007 admin

— 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.

Philosophy

No scientist is always a scientist

18.12.2007 admin

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.

Genetics, Joke

Why men die earlier

17.12.2007 admin

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 →

Joke, Vitamins

Link to nightmare

17.12.2007 admin

Sorry, I have no permission to reproduce any of the photos here but you can check the links below for some cod liver oil photos
nightmare | double use | evil woman.

Philosophy, Software

Research not re-search

16.12.2007 admin

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

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 ;-)

Allergy, Vitamins

Hans Selye: Ancestor of the allergy vitamin hypothesis

14.12.2007 admin 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 →

Genetics, Software

Annotation of regulatory sequences is largely insufficient

13.12.2007 admin

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.

Genetics, Software

Anonymizing genetic data

13.12.2007 admin

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 companyâ€™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 →

Joke

First we take Manhattan

12.12.2007 admin

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

Genetics, Software

Genome explained

12.12.2007 admin 1 Comment

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 →

Allergy

Is hayfever contagious?

12.12.2007 admin

At least some researchers believe that hayfever is contagious.

Only last week, however, I found this advertisement in Science (April 18, 1890) – so this is not a very new concept. (there is an old saying that obsolete theories only die with their proponents, ;-) Continue reading Is hayfever contagious? →

Allergy

Rural protection or urban living

11.12.2007 admin

A paper in Pediatr Allergy Immunol asks this question – and it is one of the best questions to ask. Given my sceptical view of farm related explanations I find relief here

The negative association between rural living and the risk of atopy during childhood, which is independent of farming practices, implies that it is mainly driven by an urban living effect.

Allergy, Vitamins

A, then E, then B, then D, and then again E

10.12.2007 admin

I have just completed an ultra short letter to JACI on a confusing vitamin D article Continue reading A, then E, then B, then D, and then again E →

Philosophy

The only point of contact

10.12.2007 admin

Steven Pinker complains in this week Nature about the recent review of his book “Stuff of Thought“.

The fact that I (like most cognitive psychologists) have not signed up to these views is the only point of contact between my book and her review.

While Pinker could have got at least his opinion through, my comments on ORMDL3 remained stuck although I also claimed that the authors of this paper

free-associate to her own beliefs.

Yea, yea.

Allergy

Endocrine disruptors

10.12.2007 admin

This is a topic occasionally popping up (frequently after some spectacular press article) but there doesnÂ´t seem so much systematic research. Only recently I came across an article on plastic additives and surfactants (alkylphenols) that can suppress Th1 development – so is plastic the “Western life style factor”? The only other study that I have heard before is about benzophenone, octylphenol, and tributyltin chloride (TBT).