Cambridge University Peter Murray Rust discovered he cannot have access to his article he paid for an Open Access publication in an Oxford University Press journal. This caused some discussions on /. but, as usual, it’s better to first have a look at Peter Suber blog to have an objective view on this.

I’m wondering why Sun chose Derby for its JavaDB … I used JavaDB on a project and my main reason was that it’s embedded in the last Java Runtime Engine (JRE). But I saw a clear degradation of performances (my main criteria is speed) when I had to access the embedded database. And it became worst when I ran my project from a CD-ROM (because it has to be distributed). So I decided to run a small, rough test and compare JavaDB with two other free Java database engines: H2 and HSQLDB. And the results are astonishing: JavaDB seems to be the slowest, hence the worst choice (except for the license). Here are the results (click to show the normal size graphs): ...

There are many websites around that allow you to download videos from YouTube. But it’s not possible to do it directly from YouTube. And you end up with a proprietary Flash video file. Although you can install the Flash plug-in on your computer, there are cases when you don’t want to do so or you are even not able to do so. So, for whatever reason, you want a video from YouTube on your computer in a file format suitable for any kind of multimedia viewer? Here is a small (15 lines) bash script to download and convert a YouTube video you like in standard MPEG format. For that purpose, you’ll need wget (usually, you already have it on your GNU/Linux box) and ffmpeg. ...

In the last post, I told you one of my photo on Flickr was published in an article from Nature Reports Stem Cells. After some discussions with three friends, I decided to write an e-mail to the journal editors basically stating that, although I enjoyed my photo being shown in their journal, they did not comply with one of the two conditions of the CC-by-sa license (the “Share-Alike” part, more details in the copy of my e-mail). I chose this licence for this photo because it is there to give freedom to other people on some material while this freedom stays with the media even if the latter is modified. ...

I was very pleased to see my first publication in Nature( 1), the scientific journal with an impact factor of 26! Well, it’s not really what you can expect (especially if you are one of my two mentors): one of my photos on Flickr, representing a rat eating (or praying?), was chosen to illustrate a summary of UK Academy of Medical Sciences report on animal-human chimeras :-) Click on the thumbnail above to see the full screenshot ...

Things are better now: Nandini is back, ankle is better (not 100% though), parents-in-law moved into their new home and all the family is fine :-)

Someone hoped my laptop doesn’t make too much noise after I posted a photo of the Tecra logo on Flickr. The short answer is no, it doesn’t make too much noise. At 10cm from the fan output, I can measure 42 dB when the fan is off and 52dB when it’s on. Beside the fact that I don’t hear that noise when I have my headphones, it was not sufficient for me. I wrote small python and gnuplot scripts to collect and display temperature, fan status and load ( .tar.gz file, 1.3ko). During those 2 hours, I checked my e-mails, read news on the web and wrote the OPML output in catrss (that’s why load averages increase at the end, when I’m debugging the software). Here are the results (click on an image to see a larger version): ...

A few days ago, I released the first version of catrss, a tool used to concatenate RSS file(s) to standard output. Today, I added OPML output to this tool. Here it is in version 0.2 (.tar.gz file, 16ko). OPML is a file format first used in a commercial application. Now it’s widely used for the exchange of links between news aggregators. Because of that, I had to implement it in catrss: it’s a potential format for the output of catrss. ...

I’ve just released the version 0.2 of Picklist Editor. Now you have a table of all the proteins on the right of the gel. If you double-click on a cell, you can edit it (note this is not a recommended behaviour). After revalidating the table, your new spot will be included in the gel (and saved to your picklist if you like it). For me, this version is stable and fully functional :-) ...

This morning, I released Picklist Editor 0.1 with a text introduction … Hmmm … on my photos on Flickr you can see the hardware side of the picking process … (click on pictures to see details). On the photo on the left, you can see a gel on a low-fluorescent glass plate. This plate is in part in a tray that firmly holds it when the robot is doing its job. The holes everywhere result from the picking process but there are proteins everywhere and you can’t see them in visible light since they are labelled with fluorescent Cy dyes. You can see two white round stickers on each side of the gel: these are the picking references. ...