Notes from the biomass

Youtube links were about the last thing I thought I’d ever blog. But the lab tour of the Knight & Eddy labs at the MIT are highly suitable for Friday nights and Monday mornings alike. [via]

Nature Biotech has opened a new section, Community Consultation, which aims to involve the scientific community in the development of standards for publications. The first manuscript for review discusses The Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx).

The authors comprise many important people in the interacting proteins field, both experimentalists and bioinformaticians associated with the development of databases such as DIP, BOND and Intact. One important focus is to enforce unique identifiers for biomolecules; I was pleased to see that the experimental role (such as “bait” in a biochemical purification experiment) is enforced too, as it was missing from many databases and is often neglected in bioinformatics network analysis.

The bioinformatics community will benefit from these standards most. Let’s hope that all publishers will enforce them consistently.
[Via Pedro Beltrao. Nature could really give this broader coverage, they should be proud of it.]

Any sufficiently advanced technology is indistinguishable from magic as long as you don’t use it in your everyday work. In the sciences, there is hardly anything left that I would consider magic devices - instruments that fascinate me because they contradict my daily macroscopic experience. Mass spectrometers are a notable exception. Working in the vicinity of these instruments for several years and probably having understood how some of them work, the results these instruments deliver still fascinate me.

There are other applications to mass spectrometry in biology than identifying proteins, I sometimes have to remind myself. In a recent article in Journal of Biology Claude Lechene and colleagues describe a new instrument that uses stable isotope mass spectrometry for imaging cells in unlabeled samples.

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The Archon X-prize for genomics was finally announced yesterday. It will be awarded for a technology that can sequence 100 individuals in 10 days. Venter’s $1000 price tag seems to have been dropped though. The BBC reports that the genomes of wealthy individuals/supporters will be used (the X-prize press releaseisn’t all that clear on that issue). The first 100 individuals are to be chosen by the contestant, the next 100 from a list of famous people selected by the X-prize consortium, as the NYT reports.
The focus on the individual as the source of the genomic material strikes me as a silly contribution to the debate on how public your genome sequence should be. But the debate on the ethics thereof will be put to rest once genome sequencing begins big scale and becomes a commodity. About then, people will publish them next to their vanity picture in the upper right corner of their blogs (my picture, about me, my sequence).

[via]

N.B. Bio-IT world has a noteworthy commentary on the controversy around “celebrity sequencing”