Heng Li has an excellent overview table on next generation sequence alignment viewers (as well as alignment programs) – thanks to TB for pointing me to that site. The Broad Institute has just bought another 30 Illumina Genome Analyzer – they now own 89 so the Broad people might have clearly a need for visualizing data.
The best choice is not easy to make – I am trying now the IGV in my lung sequence project. Annother interesting piece of software not listed by the Heng Li table is annoj that looks promising too, yea, yea.

Here is another paper that supports my long-standing view that the hygiene hypothesis may be wrong

We identified 3626 participants of the European Community Respiratory Health Survey II in 10 countries who did the cleaning in their homes and for whom data on specific serum IgE to 4 environmental allergens were available …The use of bleach was associated with less atopic sensitization (odds ratio [OR], 0.75; 95% CI, 0.63-0.89).

yea, it says less not more! And there is another paper that ask about the hygiene hypothesis “Do we still believe in it?”

This has little relationship with ‘hygiene’ in the usual meaning of the word. The term ‘hygiene hypothesis’ is unfortunate, as it is misleading. A better term would be ‘microbial deprivation hypothesis’.

I even think that microbial deprivation is questionable.

An interesting piece published in Science finds that

The accuracy and predictability of a hypothesis depend on the validity of the inputs used to generate and test it. Because problems are typically complex and information regarding their solution is limited, the solution is more likely to be found if the information base is greater. This rationale is a driving force behind systems biology, which attempts to define biological complexity from a systemic perspective using information technology … High-profile journals publish systems biology studies, including the human genome sequence, but most papers focus on hypothesis-driven investigations.

The most remarkable point here is the fact that there are still more people who believe in an underlying truth. This reminds me to the philosopher (Show me more…)

The new BMJ has an interesting letter on current vitamin D research

We are concerned that, in some areas of medicine, too much emphasis is placed on analysis and reanalysis of a limited amount of trial level data, rather than on the design and conduct of informative RCTs in relevant populations.

yea, yea.