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.

I wanted to see how it works. But since I’m temporarily stuck with a Windows laptop, I downloaded a free C++ compiler for Windows (wxDev-C++), imported all the files in a project and compiled. For those who want to try, here is the project file and the specific makefile in a zip file (2 kb). Just decompress the FluTE archive (I used version 1.15), copy the two files from the zip file above and launch the IDE. In the project options (Alt+P), specify the custom makefile (in the "Makefile" tab) as the one from the zip file above. Compile (Ctrl+F9). Done.

On my Intel Core2 Duo T5450 (2Gb RAM), it took 6 minutes to simulate the "two-dose" example.

Please note that I didn’t try to compile with OpenMPI. Maybe for next time.

I didn’t see that before but came to know when I downloaded the 453 remaining e-mails from an old account (3 months without fetching them). The announcement of this new impact factor was in one of the three interesting e-mails.

Redesigned Pubmed homepage (bigger image)

Redesigned Pubmed result page: search box is hiding the logo, the display settings and the first result (bigger image)

To be fair, I must say these screenshots were taken with Firefox 3.5.3 on Fedora Linux but I didn’t see this problem with other operating systems nor other browser (not even Firefox on MS-Windows). Seems they tested their design with everything except Linux (A search with Pubmed redesigned doesn’t work with text-only browsers although the previous one perfectly worked)

Slowly, slowly, most software on my website will be hosted on Sourceforge or Bioinformatics.net.

P.S. Obviously I chose the time where they are in the middle of a large scale site changes and upgrades so nothing is available for now (except the screenshot).

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).

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.

Recently, Garr came back on the Ignite presentation style with a presentation from Pamela Slim. Here is a video recording:

I maybe liked this presentation for its content but above all for its style … At Ignite, you can have a maximum of 20 slides that automatically advance every 15 seconds (so max. 5 minutes talk). I like this kind of challenge. Unfortunately, there is no planned Ignite event in Western Europe soon where I would be able to watch this live.

Finally, I still have to find a way to use this kind of presentation (large images, few words) in a scientific communication (who said PhD dissertation?) where precise facts and figures are often more important than concepts or message. Maybe just because scientific presentations are often meant to share measures, quantitative observations, statistical data, etc. For a communication that will show a review of the literature on a subject, this style would fit better.

Following this, I had interesting discussions with my dad about sleep patterns in babies. It could also be interesting to hybridize what we did for Gemvid and this simple solution in order to be able to quantify human/baby movements during sleep. My little knowledge of OpenCV can then come in handy for the motion and pattern detection …

Some additional technical details : Video was made from 321 TV screen captures (1 every 2 minutes) and played back at 1 frame per second. It was converted with FFmpeg (LGPL) and the Flash player is JW FLV Media Player (CC by-nc-sa). Ok: Flash is not free.