Notes from the Biomass

Using Wikis to share information within a research group or in a collaboration becomes more and more frequent, even if many scientists haven't heard much of Wikis beyond the 'pedia. Openwetware is another endeavour by several groups to exchange information on ongoing projects and protocols.
However, it is different in many respects in that there is no formal collaboration between the participating labs, yet all pages are open to everyone under a Creative Common License.

From their current boiler plate:
OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology. OWW provides a place for labs, individuals, and groups to organize their own information and collaborate with others easily and efficiently. In the process, we hope that OWW will not only lead to greater collaboration between member groups, but also provide a useful information portal to our colleagues, and ultimately the rest of the world.

Most of current members are labs from the MIT and the UT Austin;Bioinformaticians will probably have heard of Chris Burge's lab. Others are invited to join which is as easy as sending an email. As far as I can see, there is no particular focus of research groups, but synthetic biology seems much discussed and technological development is a more of a focus then intricate details of well studied fields of biology. It does not appear that openwetware is widely publicized currently - only the del.icio.us link of a member pointed me to the site. It's bold step to make all the material available, even if concrete research results must cannot be publized yet. Let's hope the site goes well and other groups follow up on making research more transparent.

Groucho Marx said: "Time flies like an arrow, fruit flies like a banana." He's wrong. Time flies like a banana. It runs out quickly and you return to where you began. Fruit flies probably like arrows too.

[Thoughts when you realize that your blog was vacant for a week. ]

The company (and university) lawyers will have to fire people now: only 20% of the human genome is claimed by patents, a recent report in Science finds. The authors run BLAST to map nucleotide sequences from patents to genes and their analysis is geared towards a high specificity and is restricted to human sequences. Many patents try to cover more genes, also using insights gained in model organism, so the number given is only one amongst many plausible answers.
At the end of the day, the patent holder will have to convince a court that the information of the gene sequence enabled some one else to generate profit. Do you need to know which gene is actually targeted by your novel drug when you started working on a particular disease?
[Thanks Jason]

A review of the current state of open access publishing concludes that Peer review and copy-editing may be less rigorous with Full Open Access journals, amongst other controversial findings.
In the light that many of the organizations who requested the report publish under the traditional model one might want to question the independence of Kaufman-Wills, a consulting firm specializing in electronic publishing. The Scientist's feature (which notified me of the report) lists other questions and perspectives on the report, including the opinions of open access activists.

More than once, I critized PLoS for changing only the access to publications rather than offering an enhanced way of scientific communication. At least one of the standard features of most content management systems - the ability to add comments - will now be used for all PLoS journals. The aim is to add real correspondence, not just "I like this papr. Good vork. Yours Schnuffelfred", hence the "electronic letters" will undergo editorial screening. As of now, you have click links in the sidebar to find out whether there are "eLetters", which is a little annoying but I am sure there will be enhancements. A selection of letters is supposed to appear in the monthly journal.
The editorial of the current issue has more details and specifically mentions blogs as an influence.

[N.B.: Of course, there is a page to see all eLetters.]

After Nature, my favourite scholartainment magazine, started blogs (which I fail to find after the recent site redesign), offered a toolbar and the social reference manager Connotea, the podcast, which was started with the current issue, was a foreseeable extension. I have not much use for podcasts - I don't listen to the radio much at all and I usually cycle to work, when most people listen to it, I guess. Anyway, I downloaded the hefty 20 minutes and listened. The 'cast is presented by the ungooglable Dr Chris Smith. We get reviews of recent scientific publications, commented and explained in a rather light hearted manner and augmented with interviews with the scientists. I like the personal note of the interviews really. The selection of topics is suitable to a wide audience of scientists but I was surprised that the Nobel prizes that were announced on Monday and Tuesday were not part of the Wednesday show - I guess, the medium needs a little more independence and more spontaneous action - announcement of the prizes caught somebody by surprise.
Let's see how it develops - 20 minutes is a little long for my attention span, so a handful of shorter podcasts, spread over the week would suit me better. May be I should also buy that iPod Nano finally.