Tag: science

An update on JoVE

Three years ago, I wrote about JoVE, the Journal of Visualized Experiments. JoVE was a peer reviewed, open access, online journal devoted to the publication of biological research in a video format. I recently discovered that since 2009, JoVE is now just a peer reviewed, ~~open access,~~ online journal devoted to the publication of biological research in a video format. You can debate at length on whether JoVE was Open Access (as I thought) or not. I just think it’s sad although I understand their motives: in a recent exchange with them, they wrote they “handle most production of our content [themselves] and it is a very very costly operation”.

The recent exchange I had with Jove was about another previous post describing a way to store the videos locally, as anyone would do with Open Access articles in PDF format. I was unaware of two things:

JoVE dropped the “Open Access” wording as I wrote above (however, there is still a possibility to publish a video in free access for a higher fee, as described as “Open access” in the About section for authors);
the “trick” was still working (and people at JoVE seemed to be aware of that and I saw similar description of the trick elsewhere).

Unfortunately, this trick will not work anymore in the coming weeks since they will “do token authentication with [their] CDN“. JoVE will remain for me a very interesting journal with videos of quality and without any equivalent yet (SciVee doesn’t play in the same playground and I wonder why Research Explainer missed the comparison in their 2010 interview).

I was then wondering what could have been the impact of this decision on the number of videos published in JoVE as free access. I didn’t find any statistics related to this on the JoVE website (unrelated thought: I like the way BioMed Central gives access to its whole corpus). I then relied on PubMed to find all the indexed articles from JoVE and relied on its classification of “Free Full Text” (i.e. copied on the PubMed Central website, including the video). At the time of writing (August 2011), on a total of 1191 indexed articles, 404 are “Free Full Text”. This is nearly 34% of all JoVE articles. When you split this by year since 2006 (when JoVE went online), you obtain the following table and chart:

Year	All articles	Free Full Text articles	Note
2006	18	18	Full free access
2007	127	127	Full free access
2008	115	87
2009	217	118	Introduction of Closed Access
2010	358	42
2011	356	12	So far (August 2011)
2011	534	18	Extrapolation to full year keeping the same proportion

As we can see on the left chart, plotting the total number of articles in JoVE -vs- time, there is a steady increase in the number of articles since 2006. This tend to prove that more and more scientists enjoy publishing videos. It would be nice to have access to JoVE statistics in order to see if there is the same increase in the overall number of views of all videos. With “web 2.0” and broadband access in universities, I guess we would see this increase.

However, as we can see on the right chart, plotting the percentage of JoVE “Free Full Texts” in PubMed -vs- time, there is a dramatic decrease in the percentage of Free Full Texts in JoVE since 2008-2009. Less and less videos are published and available for free in PubMed Central. This is unfortunate for the reader without subscription. This may also be unfortunate for the publisher since there are less and less authors over time who pay the premium for free access. But since authors also pays for closed access, there is certainly a financial equilibrium.

Some methodological caveats … The PMC Free Full Texts are not necessarily in free access on the JoVE website (and vice-versa ; all the ones I checked are but I didn’t check all of them!). This might explain why there is already a reduction in Free Full Texts in PMC in 2008 while JoVE closed their journal in April 2009. I expected the same proportion of free articles published until the end of 2011 than in the beginning of 2011 ; this might not be the case (let’s see in January 2012 ; this also leads to the question: “is there a seasonal trend in publishing in JoVE?”).

What I take as a (obvious) message is that if authors can pay less for the same publication, they will, regardless of how accessible and affordable the publication will be for the reader. I don’t blame anyone. But I can’t help thinking the Open Access model is better for the universal access to knowledge.

Photo credit: Sorry We’re Closed by Cinderella on Flickr (CC-by-nc-sa)

"Facts & data"

A colleague of mine is always hammering home the message of bringing facts and data to a discussion rather than rumors, hearsays and daily newspaper articles. Since a few days (because H1N1 is not a pandemic anymore?), newspapers are coming with another “Superbug” or “Germinator“, wrongly named “NDM-1“. So, before spreading fear, uncertainty and doubt, please read the scientific litterature or, at least, read quality newspapers (articles from The Guardian are quite fair and balanced).

NDM-1 (New Delhi metallo-beta-lactamase) is just the name of a gene in a plasmid that two bacteria at least, K. pneumoniae and E. coli, can carry. This gene makes bacteria resistant to almost all antibiotics. If you want to know more about this gene, Yong’s paper characterised it (access without subscription). Health care agencies know about this issue at least since last year.

Now, you can still go to India and Pakistan. New Delhi is still a safe city to visit. But yes, in general, the world will face a problem in the future because bacteria are becoming resistant to more and more antibiotics.

About file formats accepted by BioMed Central

BioMed Central is one of the main Open Access publishers in the world of Science, Technology and Medicine. On a side note, that’s where I published my two articles (in Proteome Science and the Journal of Circadian Rhythms). One might think that, given their support to Open Access, they would also support Open Source software and Open Format documents.

For the software side, it’s not very clear. Although they ask authors to consider releasing software described in publications under a free (or at least open source) license, they also support and advertise for a bunch of proprietary software. While it’s not a bad thing per se (it enlarges the number of potential authors), it’s sad to see they don’t cite popular free software like OpenOffice.org (to write your article), Gimp (to edit your figures) or Zotero (for reference management). These are the three main software in each category but the free software world has many more of them!

I decided to write this post because I recently received an e-mail from BioMed Central stating that BMC Bioinformatics, one of their flagship publications, accepts a variety of different file formats in the submission process. This was already true when I submitted my articles. I wanted to know how they improved their submission process in this respect and if they now added open document formats (in a broad acceptance, not only the OpenDocument format somehow linked with OpenOffice.org).

E-mail from BMC Bioinformatics with file formats accepted for submission

My first comment is that the list of accepted file formats usually applies to all BioMed Central journals, not just BMC Bioinformatics, since they share the same publication platform. In the Instructions for Authors, the following file formats are accepted: Word, RTF and LaTeX (with the BMC template) for text, EPS, PDF, TIFF as well as PNG, Word (sic), PowerPoint (re-sic), JPEG and BMP for figures. In addition, they list CDX and TGF to represent chemical molecules. How disappointed am I!

I’m disappointed because some interesting open formats have been left out. And I can’t find interesting links stating that BioMed Central will support them soon.

With some stating that OpenOffice secured more than 15% of the business office suite market as of 2004 and despite an ISO standardisation (ISO/IEC 26300:2006), the OpenDocument formats are still absent. Many young scientists now use OpenOffice.org because it’s free (mainly free like in free beer, though), because labs can’t afford MS-Office licenses prices, even educational ones but also because it allow them to do everything they want. I agree that you can easily convert your ODF, ODS or ODP documents into their respective proprietary DOC, XLS and PPT. But it would have been nice to directly have the ODx documents. On the technical side, ODx documents are “just” XML files: tools exist to automatically parse them and transform them in the journal final format (I didn’t write it’s easy but it should be more easy than reverse-engineering closed, proprietary file formats).

I’m also disappointed because although the PowerPoint format if there, SVG is not. I guess it’s just because they only use bitmap versions of the PowerPoint files. All vector graphic editors supporting SVG (and all of them support SVG: Adobe Illustrator, Inkscape, Dia, …) have conversion functions to bitmap equivalent of your drawings. So it may have little impact. But it would have been better if BMC support for SVG was direct.

In conclusion, I’m hoping the extraordinary work done by BioMed Central in the publication area will extend to the formats they accept for submission. A partial example could come from PLoS submission guidelines (here for PLoS Computational Biology, especially for figures) where they explain a lot of technical as well as license aspects and cite free software as reference.

E-conference about scientific patents

While looking for pictures related to patents, I found these interesting ones taken by Daneel Ariantho on Flickr. They depict a virtual conference about scientific patents. It could be interesting to get more information about 1) the content of this conference and 2) the kind of conferences organized in these virtual worlds. It could also be interesting to see the social aspects of these conferences (are your contact better/different in a virtual conference?) and the “quality control” (of speakers, of posters, of advertizers, …).