Notes from the Biomass

Usually, the posting and comments on scientific subjects at Slashdot reflects the broad spectrum of its readership. This thread on Open Access publishing is definitly worth reading.

The Wired story that the Slashdot post refers to Is also worth reading to find a nice overview of pros and cons.

Nodalpoint hosts this comment, describing the requirements of the young PI for his new position - I have heard many people talking about such matters recently, and (as a young PI), was a little amused. The more you push such questions, the less you will get - your superiors need to be for you, or you should not join. The competition should be between the people wanting to get good people, not the other way round.

Even "competition between the ranks" is not a real show stopper, as long as it is not very destructive. If the environment is of substantial size, competition is unavoidable, after all, there's only one first author.
As a PI you need to be in a supportive environment (check), have access to computing resources (check - I have to share them but don't need to administer them...) and be able to draft the project that The Authorities (your dep head or the grants) support. If you fail, you shouldn't start anyway.

Recently, I stumbled across this paper that describes an approach to predict the localization of proteins in yeast.
I was suprised and giggling in my chair, because the whole yeast proteome was screened for its localization by Huh et al. , so why would any body agree to publish such a method. Obviously, the study by Huh et al. fails to get a signal for each and every protein due to experimental reasons. Some proteins are simply not accessible and the authors of the computational study simply fill the gaps.
However, it appears to me that the task feels trivial and wonder what bioinformatics, at least the part that's want to predict biolological properties. So far, no method was really good at predicting the localization from sequence but the task appears simple compared to fold prediction - which has been predicted (by David Baker, if I am not mistaken) to be good once all the folds have been discovered experimentally.

I wonder, whether there will be bioinformatic predictions of real impact. Can you name a few?

This is my 'professional' web log, containing information that I would like to share with others interested in 'professional' bioinformatics.
There are other interesting web logs dealing with bioinformatics out there - this one will serve as my notepad, link list and as general margins on where to scribble my thoughts.

My research focus is comparative genomics, host-pathogen interaction and a good deal of classical sequence bioinformatics.