Month: December 2005

Quaero and the quest for alternatives

An article in the French newspaper Le Monde presents Quaero (to seek, in Latin) as the future “European Google”. Comments on this article are divided between supporters of this alternative and denigrors that predict another bureaucratic, bloated, ineffective project. My point here is not to argue pro or against this project. But I would like to dwell on American databases and search engines that serve the entire world.

When you need to look at some information on the internet (mainly, the web), I am sure you are using (American) tools like Google, Yahoo! or Altavista. In the life sciences domain, we have a wonderful database, PubMed, a service of the (American) National Library of Medicine that includes over 16 million citations of biomedical articles. When you are preparing a presentation or an experiment on a subject, it’s a great tool to do the bibliography.

I am insisting on the fact that these tools are coming from American companies or government agencies because I am wondering what we are going to do if, one day, for whatever reason, the U.S.A. will decide to stop providing these tools to the entire rest of the world. Or what if they simply decide to filter content delivered outside their country? Are you sure they are not already doing it? It’s the same problem with the satellite positioning system (GPS ; that’s why Europeans are launching the Galileo project), the root of internet domain name servers, the Microsoft Windows operating system, etc.

So, if the goal of Quaero is to achieve a relative independance, I agree with it (I have still some fears it will become a costly and ineffective tool). But I am wondering why isn’t there any free (at least as in “free beer”) alternative to PubMed. For the moment, I only see an alternative in the cooperation, interoperability between Open Access repositories with projects like the Open Archives Initiative, OpenDOAR, GNU Eprints and other software. But, until Open Access journals are widely used by scientists, it won’t be a PubMed replacement. And there is still no alternative for scientific litterature already published in Closed Access journals.

Identification -vs- authentication

I was reading a presentation on the Belgian electronic identity card (PDF 150 kb, in French, by a friend). Compared to the old, analogic card, this new card has an electronic chip on it. This chip contains some information that are already visible to any human eye on the surface of this card and more information (like a photo, your address, digital certificates, …). I stopped on the 5th slide where it’s said that this new “e-ID” will allow someone to be identified, to authenticate (what?) and to fill in on-line administrative papers.

Being in the “general culture” of privacy-related subjects, I often heard these two words (identification and authentication). But I never paid too much attention to their meaning. So, once and for all, I decided to have a look in a dictionary.

Identification is the act or process of identifying somebody or something or of being identified. So, it’s an act or process of showing or proving who somebody is. The identity card (ID card) is a card bearing the holder’s name, signature, etc. and often a photograph, carried or worn by somebody to show who he/she is.

Authentication is the act or process of proving something to be valid, genuine or true (act of authentication). You even have the word authenticity, the quality of being authentic.

So, why put identification and authentication means in the same card? Aren’t they redundant? The old, analogic ID card was sufficient to prove who I am to a policeman and to retrieve administrative documents. I think the idea behind this new e-ID card is to adapt this identification process to the electronic world (internet being the most obvious one). It seems it’s far more easy to forge another identity based only on character strings and bits than on a real, physical human being. When paying on the internet with a credit card, you need your card number, your name and a “validation number” that is on the back of your card. Now, with the e-ID, you’ll have digital certificates to electronically identify yourself and authenticate this identification.

As I use to say, this is only a tool (like a hammer, a knife, a RFID tag, a video camera, etc.). But now, I often add that it depends on the goals behind the creation of the tool.

A knife was first created to cut meat, branches, etc. A hammer was first created to hit on a nail. A video camera was first designed to add motion to photographs. Now some people use knives to take control of planes, they use video camera to film their children playing around or British cars registration numbers. This diversion of usage, combined with an increasing “Western comfort” lead some people (in governments or not) to the need of preserving this comfort, this security. They now not only created new tools (DRM, RFID, …), they created tools in order to keep and further increase their profits, to control identities, …

I am not saying that the Belgian government is intentionally imposing the e-ID card in order to control Belgians. But, apparently, some points are not clear … Who will control who (or what application) will have access to the information stored on the chip? And who will control if the restrictions on information access are respected (and how)? Who will control data mining done with information retrieved from the chip (and how)? For the moment, only information already available from different sources are now grouped on the chip, making them easier to retrieve. Who knows what kind of information could be added on the chip, later? If you want more information on this topic, I suggest you to follow the news on the AEL website.

P.S. I really like dictionary: you are looking for one word and you finally read definitions of 2 or 3 words. And if you have an illustrated dictionary, you’ll also look at the pictures. For example, in my Oxford dictionary, “identification” is on the same page than an illustration of an iceberg. An iceberg is just “a huge mass of ice floating in the sea”. But, because it’s related to the idiom “the tip of the iceberg”, nearly 80% of the illustration is showing iceberg part below the see level. By the way, while I was there, I also checked the word idiom: “a phrase or sentence whose meaning is not clear from the meaning of its individual words and which must be learnt as a whole unit” (of course, I also read the other definitions of idiom …).

GNU/Linux installation and usage: prejudices are hard to fight

Regarding GNU/Linux installation and usage, prejudices are still hard to fight (at least in my environment). Yesterday, we had the usual Christmas dinner with some friends and family. At one moment, talks went on technology, computers, peer-to-peer, etc. One of the boys just bought an Apple Powerbook and his wife got a laptop PC from her work (MS-Windows only, of course). We ask them to put GNU/Linux or, at least to try free software. For their general usage, (writer, calc and impress), The Gimp, FireFox, Thunderbird, … are sufficient. They don’t need more: specific applications they might use are already on dedicated computers in the laboratory.

The three main prejudices, reserves about GNU/Linux are:

  • It will be difficult to install
  • It will be difficult to use and they don’t want to type 1000 lines of commands
  • They won’t be able to communicate and share documents with other people

First of all, GNU/Linux is not difficult to install. Free software are related to freedom and choice. You have to the choice. You can choose a GNU/Linux “flavor” (aka. distribution) that is very easy to install and yet powerfull enough (e.g. Fedora Core, Mandriva, SuSE, …). I personally installed the Fedora Core on two computers of mine and my wife’s laptop. The only thing that I needed to know is to click on the left button of my mouse and to enter my name and password at the right moment (that is: when the computer asked to do it). Of course, you can choose to have a more difficult installation. Just choose the “advanced installation” option while installing the distribution cited before or you can also choose a distribution often considered less easy to install like Debian.

And GNU/Linux isn’t difficult to use and you have the choice for the 1000 lines of commands. Everything you can do with a mouse with MS-Windows, you can also do it with a mouse with GNU/Linux. In my opinion, you can even do more with GNU/Linux since there are a lot of free software available. I am sure that at least one of them will fit your needs.

Finally, why an operating system will deprive you from sharing your documents with other people? If you think that MS-Word documents are a “standard”, you are wrong. But if you still want to open .doc files other people sent you, just open them! writer can do it, Abiword can do it, antiword can do it, …

Just try GNU/Linux (Ubuntu and Knoppix are GNU/Linux flavors that doesn’t need to be installed on you computer). Try it for at least one month (I am not saying to use it 24hours a day, 7 days a week, go progressively if you want or if you don’t have time). And then choose. And whatever you choose, please give Microsoft or the GNU/Linux community your feedback. I don’t know if Microsoft will listen to you. But I know that the GNU/Linux community will hear your well constructed arguments against or pro GNU/Linux and try to improve it.

P.S. Oh, yes: Merry Christmas to you all! 🙂

Scientists find a "sweet tooth" in the (rat) brain

Researchers at the University of Michigan have found a “pleasure spot” in the brains of rats that may shed light on how food translates into pleasure for humans. The spot in rats’ brains makes sweet tastes more “liked” than other tastes. So now I know what’s going on when I am eating sweet Indian pastries :-p

Reference: Peciña, S. and Berridge, K.C. “Hedonic hot spot in nucleus accumbens shell: where do mu-opioids cause increased hedonic impact of sweetness?in J. Neurosci., 25: 11777-11786 (2005). On Berridge’s web page, you can also view a cool video illustrating this subject.

Where am I? – Où suis-je ?

If you used to see me on MSN or Yahoo!, there is a risk I won’t be there anymore. I’ll now try to only use the free Jabber protocol. If you want to know more about jabber, please have a look at the Jabber overview. Clients (software) are available for MS-Windows, Linux, MacOS, etc. ; see here for a list of software (with some of them, you will even still be able to chat with your MSN and Yahoo! contacts). My Jabber ID is jepoirrier at

Si vous aviez l’habitude de me voir sur MSN ou Yahoo!, il y a un risque que je n’y sois plus jamais. Je vais maintenant essayer d’utiliser seulement le protocole libre Jabber. Si vous voulez en savoir plus sur Jabber, jetez un coup d’oeil à cette introduction (et les premiers pas associés). Des clients (logiciels) sont disponibles pour MS-Windows, Linux, MacOS, etc. ; voyez ici pour une liste de ces logiciels (avec certains d’entre eux, vous pourrez même continuer à communiquer avec vos contacts MSN et Yahoo!). Mon identifiant Jabber est jepoirrier chez

Strange things with Poseidon for UML 4.0

Gentleware recently released version 4 of “Poseidon for UML” (an UML modeling tool). They said it now respects many more features of UML2 but I am not proficient enough in UML to clearly see all the advantages. But there are still some strange things. Two examples:

1. The default graphics format of Poseidon installed on a Fedora Core 3 is PNG. The default graphics format of Poseidon installed on a Fedora Core 4 is JPG (same with SuSE). I tried to look in the config files (in fact, in all text files in the installation path) but I didn’t find anything related to this topic. It’s probably an OS default setting but I didn’t had the time to check.

2. SVG export is still very “basic”. Indeed, each graphical element isn’t connected to any other element, without any coherence. For example, a class is represented by 4 independant objects: a rectangle, a text for the class name and two lines. Nothing is even grouped! You’ll find an example below. It’s sad because if they simply grouped their objects (e.g. all the graphical objects belonging to the same class), it would have been much more simpler to do final last-minute small modifications to the exported graphics. I don’t know if it’s in the SVG standard but Inkscape now supports “connectors”: graphical objects can now be connected using auto-routing lines. If it’s in the standrad, Gentleware could have used this option.

Edition of a Poseidon SVG export in Inkscape

2 studies, 2 differents vision of innovation and competitivity in Europe

Some days ago, IDC published a study carried out on behalf of the BSA (Business Software Alliance). In this study, they promised the creation of 4 000 new jobs and the addition of 2.6 billion US$ to the economical growth in Belgium if software piracy is reduced by 10% between 2006 and 2009. For France, it is a promise of 30 000 new jobs and an addition of 13.7 billion US$ to the economical growth!

Although I know which companies are “hiding” behind the BSA (Microsoft, Adobe, …), I think that this continuous battle against software piracy could only be a benefit for the free software industry. With exceptions of some job-specific software, I think free software have now all the capacities to be used in the industry (imho ; and there are software which are only available as free for some jobs). Therefore, to oblige people to acquire licences is also, in a way, to oblige them to ask themselves questions of costs and dependences to their suppliers. And, perhaps that the idea of a migration to (or to remain with) free software can be seriously taken.

On the “other” side, a study on innovation and competitiveness in Europe (PDF 1.8Mo), carried out by PricewaterhouseCoopers on behalf of the Ministry for the Dutch Economic affairs, presents the future European law on the patents as a particular threat for the ICT industry in Europe. The study takes in example the rather moderate protection set up around IP protocol, the www, Linux, … (discoveries made in Europe) which made it possible to maintain a “competitive and innovating” software industry while limiting the entry of new actors on the market. However, according to the study, the nature itself of the patents could kill the innovations rate/rhythm in communication and information technologies. In conclusion, this study also identifies 10 potential important technological progresses and recommends to the European Union to lower the barriers of entry on the ICT market and to encourage the investment and the standardisation.

Linux, interoperability, standardisation, position on patents, … I prefer this study by PwC and you?

(J’ai également publié ce mot en français sur LinuxFr)

Animal housing unit inspection :-)

This afternoon, the secretary of the university ethics committee came to visit (inspect) our animal housing unit. We (and I) can be proud of our work since he said quite a few times that we have a “model” unit, a unit that is clean, etc. 😀 As I said before, the animal wellbeing is one of the top priorities in the lab. And it is always good to be congratulated for our work (since I am working alone in my unit, it doesn’t happen often and it is even more important for me).

No network at work

Today, internet was down from 8.30 to 15.40 (I don’t know the reason). We were able to work on the local network but not further. No mail, no web surfing, no chat, nothing. This gave us the opportunity to work hard 🙂 Soon after the “disaster”, I looked for incidents on verious support websites. I didn’t find anything. But I do find some interesting graphs about the internet connection. For example:
Belnet Liege connection status
Of course, this link is completely useless if the connection is down (since we wouldn’t be able to access it). And, anyway, it’s again a geek-only concern.

Trying to use libpng

I am currently (i.e. during the night, my only free time) trying to use the libpng in order to open PNG files and process them later. I haven’t read the entire manual yet but, following their example.c, I succeeded in opening a file, check if it’s really a PNG, read all the data and display some basic information about it (width, height, bit depth, …). Next step: process the data (I will probably only be able to do it during the next week-end).