Elite young scientist

If I time this correctly, this post will be released while I am sitting at the award ceremony at Carlsberg Glyptotek waiting to receive this years “Elite young scientist” award from the Minister of Science.

I’ve been ordered not to make this award public until after it has been announced, but that should be just about now.

When I get back to Aarhus of course I’ll write some more about this.

Update: The program for the event can be found here.

Code rot?

I’ve just released a new version of QuickJoin. I just needed to add a tiny little feature, so it wasn’t that much of a deal, but I was horrified by the code. QuickJoin is from 2003 and one of the first applications I wrote in C++. The first two were QDist and SplitDist, and I dare not look at the code in those.

Did someone go in and change my code, or was I really that bad at C++ back then? Had I even heard of std::auto_ptr<>?

Social networks, Web 2.0 and stuff…

Honestly, I do not spend too much time on social networks like Facebook. I have an account there because Saskia invited me, but I don’t really go there unless someone writes a message to me.

Still, today I joined yet another such network, PLURK. In my defense, it was Amir who invited me and I was curious to see the app. he’s been working on the last couple of months. It is essentially just a timeline where you can write what you are doing at the moment and friends can keep track of each other that way.

I don’t see the point of this, but then I don’t see the point of Facebook either and that has turned out to be a succesfull business, so who knows? Maybe Amir will make a fortune on this and never have to take any of my classes after all…

RReportGenerator : Automatic reports from routine statistical analysis using R

Is something like this really useful?

RReportGenerator : Automatic reports from routine statistical analysis using R

W. Raffelsberger et al.

Bioinformatics Advance Access published online on November 24, 2007

With the establishment of high-throughput screening methods there is an increasing need for automatic analysis methods. Here we present RReportGenerator, a user-friendly portal for automatic routine analysis using the statistical platform R and Bioconductor. RReportGenerator is designed to analyze data using predefined analysis scenarios via a graphical user interface (GUI). A report in pdf-format combining text, figures and tables is automatically generated and results may be exported. To demonstrate suitable analysis tasks we provide direct web-access to a collection of analysis scenarios for summarizing data from transfected cell arrays (TCA), segmentation of CGH data, and microarray quality control and normalization.

I haven’t tried the package they describe, but it sounds like it is wrapping R for doing analysis from a GUI and then producing a PDF report from the results.

When I use R, I usually do not know exactly how to analyse my data, so it is always very exploratory and there is no way I could automate that. But then I am probably not the kind of user this package is aimed at, and I can certainly recognize the kind of R users that would be better off being sheltered from the gory details of R behind a GUI…

I don’t know, maybe I’ll try it out some time.

The citation for Research Blogger:
Raffelsberger, W., Krause, Y., Moulinier, L., Kieffer, D., Morand, A., Brino, L., Poch, O. (2007). RReportGenerator: automatic reports from routine statistical analysis using R. Bioinformatics, 24(2), 276-278. DOI: 10.1093/bioinformatics/btm556

I wonder when they’ll tell me when to teach

The new term starts next week. I will teach a course on systems biology. I have no idea when! I don’t even know if it has been scheduled yet.

Classes at the computer science department are scheduled there — I teach two courses in that department, but none of them the coming term. When the classes are scheduled, usually a week or two before the term starts, they are put on a web-page: http://www.daimi.au.dk/courses/schedules/, so the schedule is always easy to find.

My remaining classes are scheduled somewhere else, but I don’t know where. I thought it was at the faculty of science, at least I’ve been told so, but I’ve also mail the students office and was told that the classes were scheduled at the various departments. I know that we do not schedule the courses at BiRC, so now I wonder where my courses are scheduled, if at all.

On the faculty web-pages you have to be a bit inventive when searching for classes in bioinformatics. They put them under different (but I suspect random) departments. There is a heading called Bioinformatics, but that only contains the course descriptions. The class schedules are put all over the place. My last class was under biology, the one before under statistics, and so on.

I guess I should be greatful that the course descriptions are under bioinformatics — previously they (but only they) were labelled “interdisciplinary”. Only on the Danish pages, though, bioinformatics wasn’t even mentioned on the English pages.

Anyway, it usually takes a bit of web-searching to find out when to teach (and forget about using the search feature on the faculty web-page, it has never managed to find what I’ve been searching for).

This time around, my search ended up on an empty page. Does that mean that the schedule hasn’t been made yet, or that I’ve found the wrong page? Who knows?

Until I find out when I’ll be teaching I cannot plan my time for the coming weeks, and I have to schedule a few meetings.

This blows!