Blogging a thesis
April 6, 2008
Haven’t written about this (getting slack here aren’t we).
Attila is blogging his thesis. It’s certainly not going to be the last example of someone putting rough drafts or thoughts about their thesis and research on a blog or wiki, but it’s good to know some of the pioneers in this space.
Read the backstory. I also admire the thorough fact checking Attila did before taking this path.
Technorati Tags: Attila Csordas, Open Science
Open Science in name only?
April 5, 2008
Peter Murray-Rust has a post noting that Pubmed Central has serious limitations
You can’t mine the data
Maybe one should be happy about small victories, but that’s not the case here. If you can’t mine the information, then the whole exercise is pointless. In fact, if this is indeed the case, there is no victory.
Technorati Tags: Open Science, Data Mining
Peer-review and openness
March 15, 2008
This is an interesting battle. Big Pharma vs. traditional peer-reviewed publishing.
A judge ruled that peer-reviewed documents requested by Pfizer could not be released by the New England Journal of Medicine (NEJM). Personally I believe peer-review should not be closed, although I am on the fence about the anonymity of reviewers.
Technorati Tags: Pfizer, NEJM, Peer Review
Science Commons, Open Access … and affiliate marketing!!!
February 29, 2008
In association with SPARC and ARL, the good folk at Science Commons have released (under a CC-BY-NC license) a whitepaper to help scientists comply with the NIH mandate to archive their work on PubMed Central. The white paper is a good read for any scientist doing any publishing, especially the section on compliance options (Section IV).
In related news, Richard Poynder interviews John Wilbanks of Science Commons (the interview is made available as a PDF file under a CC license). In the blog post, Richard talks about John’s vision for the internet and open science
In addition, Wilbanks believes the Internet should be viewed as a platform for facilitating the free circulation and sharing of the physical tools of science — cell lines, antibodies, plasmids etc. In a sense, he wants to see these tools embedded into research papers — so if a reader of an Open Access paper wants more detailed information on, say, a cell line, they should be able to click on a link and pull up information from a remote database. Should the researcher then want to obtain that cell line from a biobank, they should be able to order it in the same way as they might order an item on Amazon or eBay, utilising a 1-click system available directly from the article.
I couldn’t agree more. That’s exactly the kind of thing I was imagining when I blogged about Assay Depot. It is also one way to monetize the open science web. I doubt John is saying that assays, equipment, etc accessed from an open science paper should be available for free. Given a semantic web of scientific information, or some form of semantic markup, which allows people to perform the kinds of actions described by John, one could think about publishers setting up affiliate relationships with vendors, perhaps coming up with one way of funding open access journals. Of course, everything will have to be on the up and up (in other words, full transparency and no special treatment for papers with affiliate vendor equipment used).
Technorati Tags: Science Commons, Open Access
PLoS Biology, TED, EOL, BIL and BioBricks
February 25, 2008
A bunch of semi-related newsitems, shoehorned into a single post.
PLoS Biology has a new Academic Editor-in-Chief, and in fellow scifoo Jonathan Eisen, they couldn’t have found a better candidate. Jonathan, who’s been an academic editor for a while, is an OA champion, a wonderful scientist, and best of all, one of the most fun people to read or meet in person.
Meanwhile, this is TED week. As anyone remotely connected to bbgm knows, TED is a favorite around these parts. Since I have already watched every video they have ever released on their wonderful website, it’s time for a new batch and voila, TED 2008 is just round the corner. Check out the list of speakers.
Speaking of TED, former TED prize winner, E. O. Wilson’s Encyclopedia of Life is supposed to finally go live this Thursday (probably to coincide with TED. Could he be one of the surprise speakers?)
Update: Looks like it’s already up
Right as TED ends, Monterrey will host BIL, the “open source” version of TED (and has been blessed by TED). I was planning to go, but other matters are going to keep me away.
At the same time, on March 1, UCSF is playing host to the BioBricks Workshop, which I blogged about earlier. I am still scheduled to attend, although that’s beginning to look a little dicey.
Technorati Tags: PLoS Biology, Jonathan Eisen, Open Access, TED, BIL, BioBricks, Encyclopedia of Life
