Part of wish list for Christmas ;-)

Since a few months, I am telling myself that I need a new mobile phone to replace my old Nokia 3410 (battery is nearly dead, some keys are not working all the time, etc.). Yesterday, Trolltech, the company behing Qt, announced the shipping of a green Linux-based mobile phone in September 2006. I don’t know if it will be a true product or “only” a development tool (a kind of prototype for developers). But I know that I want one if it’s available.

"Why groupthink is the genius of the internet"

In the August 10th, 2006 issue of Financial Times [1](*), Patti Waldmeir wrote a column about a new book [2] she recently read.

In this book, Sunstein start from a 1973 citation from F. Hayek, a liberal philosopher and economist:

Each member of society can have only a small fraction of the knowledge by all and … civilisation rests on the fact that we all benefit from knowledge which we do not possess.

While Sunstein knows the potential flaws of today internet collaborative projects (wikis, blogs, etc.), he argues that “sharing scientific information online would cure some of the worst problems of the U.S. patent system and foster innovation much more efficiently than costly patent litigation”.

Before the internet, we used to look for solutions by asking family or neighbours. Now, we are looking on the internet where people genuinely wants to communicate their knowledge. Groupthinking may be “the genius of the internet”, it already was the genius of any group, with or without computers and network.

Hmmm … Anyway, this author seems interesting to read …

[1] Waldmeir, P. “Why groupthink is the genius of the internet“. Financial Times, August 10th, 2006, p. 5 (article unavailable without subscription)

[2] Sunstein, C. “Infotopia: How Many Minds Produce Knowledge“. Oxford University Press, October 2006 .

(*) I am taking advantage of a free 4-weeks subscription to the Financial Times. That’s why it’s my second post about an article published in this journal. But I don’t think I’ll subscribe: 1. I have other things to read ; 2. business and finance are not in my core business ; 3. I don’t understand half what they wrote (especially in the “Market data” and pages alike).

P.S. When you read F. Hayek’s biography on Wikipedia, this political philosopher also made an inroad in cognitive science, independently developing an alternative “Hebbian synapse” model of learning and memory. Another interesting author to read …

Happy Independence Day!

Today, 15th of August, is the Independence Day of India. Happy Independence Day!

Happy Independence Day, pic from ISAL
Picture from ISAL

Today, the Indian Embassy in Belgium held a very small ceremony (but I was in my lab at that moment ; MS-Word invitation). I guess it is/was celebrated all over India (more pictures on the Times of India website).

Bozar India Festival, Oct06-Jan07By the way, Bozar are organizing an India Festival from October 2006 to January 2007. You’ll enjoy expositions, listen to music, see theatre plays, listen to literature, watch cinema and dance, both from old-style India and from modern India. If I have to pinpoint one event, it will be the Dhrupad concert where my father-in-law will sing with the Gundecha Brothers (dhrupad on Wikipedia). It will be on Wednesday 17.01.2007 at 20:00. But, of course, there will be many more great artists from India …

Links: Original and GEGL

While looking for something totally different (what exactly is the Mascot score? Partial answer here), I found the Original photo gallery, a two-parts tool to get digital photos on the web. This tool could be interesting for the family website I plan to build. Since my hosting company enabled PHP Safe Mode, I cannot use most on-line gallery tools. Original seems to be an ideal solution because all the treatments are done off-line, on my own PC. Then everything is loaded on the website. Still, it’s not a static gallery like the one Picasa does (for example).

I also saw GEGL (Generic Graphical Library), “an image processing library for on-demand image processing. It is designed to handle various image processing tasks needed in GIMP.” They just released a first version. ΓƒΛœyvind KolΓƒΒ₯s is also maintainer of Babl, a “dynamic, any to any, pixel format conversion library”. I am interested in all kind of (free as in free speech) image processing libraries because I’m trying to correctly open and manipulate .gel files (see problems written in this forum thread ; basically, they are .tiff files with additional tags and a different way to encode pixels).

P.S. I quickly installed and tried Istanbul, as I previously planned to do. It’s working for a few seconds of recording but then it stops. I didn’t have time to see what’s wrong (I think my resolution is too high: 1280×1024).

P.P.S. Oh, yes … And I suggested and became the new contact person for the French team for LinuxFocus. I would like to thank Iznogood for the work done before me and I hope he will stay active in the free software community. I will upload my last translations as soon as possible and try to put some pep in the French-speaking team.

"A closed mind about an open world"

Under this title, James Boyle, professor of law at Duke Law School (USA), wrote a comment article in the Financial Times [1]. For him, we all have a cognitive bias regarding intellectual property and the internet: the openness aversion. The openness aversion is the fact that we undervalue the importance and productive power of open systems, open networks and non-proprietary production. With three examples (internet, free software and Wikipedia), he somehow shows the evolution of mentalities towards theses “open things”. In 1991, scholars, businessmen and bureaucrats (and even us, maybe) would have scoffed at the internet as a business product. At that moment, control and ownership seemed the right way to go.

Now people evolved and we are a lot to love the internet, free software and Wikipedia. But the openness aversion is still there and some people are trying to restrict freedom (net neutrality, DMCA, DADVSI, DRM, TCPA/TPM, etc.).

[1] Boyles J., “A closed mind about an open world“. Financial Times, August 8th, 2006, p. 9.

P.S. By the way, I discovered Prof. Boyle and his articles on his website. I’ll now have plenty of interesting things to read (as if I didn’t already have enough article and books to read …).

Screen recording software for GNU/Linux

For a long time, I was looking for a video capture software for GNU/Linux. From time to time, I look on the web to see if there are improvements in this field. A recent NewsForge article triggered my curiosity, one more time …

If you accept proprietary formats, you can use vnc2swf : your film will be in Flash format, a proprietary format. Also based on VNC, there is vncrec that produces its own video format (this one seems to be free and easily exported with transcode).

If you don’t have VNC and are working with KDE and don’t like proprieraty formats, the recently released ScreenKast could be very helpful. This software is written by a Belgian (cocorico!) and captures your screen in a video. Supported formats are FFmpeg ones. This NewsForge article explains a little bit about ScreenKast.

But, if you don’t have VNC nor play with KDE, xvidcap can help you. And, finally, if you are working with Gnome, Istanbul is a rather new project but some parts seems to be working. If I have time this week-end, I will install it on my Fedora Core 5.

Now I think GNU/Linux has some decent screen recording software πŸ™‚

Some tutorials:

Dissatisfied with blog systems

Personnally, I am not very satisfied with current common blog systems. They are based on a huge collection of PHP scripts and MySQL but web providers couldn’t certify that service will have all the ressources needed. I am looking for something simpler, even if this solution is not (will not become) a major blog system …

Thanks to Google Cache, I was able to retrieve a nice idea Alexandre Dulaunoy had on his previous blog software (unfortunately, this idea was removed, along many others, when he changed for a new version of oddmuse). Here is the quote:

My (we)blog needs to be refreshed but I’m still looking for a simple free software to do the job. I tested various without finding a simple software backend. My requirements :

  • A vty (or at least an XML-RPC interface) interface to update the blog remotely
  • The software backend must be able to produce static pages without too much code or configuration
  • The ability to avoid spam in an efficient way (ok, the requirement moved to static pages, it would permit to avoid the spam problem πŸ˜‰
  • The ability to customize the full look-and-feel of the blog via CSS. This seems pretty simple in theory but in practise, that’s another story.

At the end of the evaluation, I came with two possible software : Emacs Muse or Oddmuse wiki engine. I’m already using Oddmuse for my messy working place. I would be very happy to get any information about possible alternative.

Some comments:

  • With a VTY interface, one can directly connect from anywhere, via telnet or SSH. It is a good idea: the software is then simple, it can be accessed from anywhere (provided you have an access to your server or you have an always-on computer that can upload new posts on the real server).
  • I don’t see exactly what Alexandre wants with his XML-RPC interface since it is only a kind of remote procedure call. If I try to imagine what he meant, the software would then be different and you will need two of them: a client (where you write your new entry, answer to comments, etc.) and a server (that will receive a message containing your entry, parse it and publish it). Of course, you can have the same software package that provides both services: a VTY interface and a XML-RPC interface
  • If you are using VIm, here is another solution to Emacs Muse: vimblog πŸ˜‰

My solution should then be this one … You simply write your entries with your favorite text editor and save it in an ad hoc directory. Every x minute/hour/day, a cron job launch the blog software. This simple software (C/Perl/Ruby/whatever) then parses the ad hoc directory. It finds small texts creation/modification date + time and rename files if needed (YYYYMMDDHHMMSS). There is a very small chance that two posts are posted at the very same second. Then it parses the files there for their content, build basic HTML files, apply a style (skeleton for HTML and CSS for style) and publish the pages to a FTP server. Plus an optional XML-RPC interface if you want.

For comments, a simple solution should be an e-mail address dedicated to the blog software. Comments are just texts sent to a special e-mail address. When the blog software runs, it also checks “its” mailbox, retrieve comments. Then, depending on the configuration, it could just append the comment to its initial post or it can ask the moderator for approval.

So, it’s not a common blog tool, i.e. it’s not web-based at all (although it could be possible to write a web interface if one whishes). It is especially well suited:

  • if you don’t care too much about your blog visual aspect (this point can be changed by adding new CSS);
  • if you have a website without PHP/MySQL and/or your website provider is too slow to process exhaustive, beautiful and huge blog engines
  • if you have access to console on a GNU/Linux computer but you don’t want to host your blog there (too little time for proper real world, secured servers configuration, not much bandwidth quota each months).

Someone to begin to code this with me?

Some thoughts about a family website

I am currently building a family website. Here are some requirements:

  1. services will be based on existing free software (I don’t have time to develop a complete solution)
  2. first service provided: a news service (I don’t know if it will be a forum or a shared blog)
  3. second service provided: a photo gallery
  4. all this should be on a shared host server (so it should work with PHP safe mode enabled ; I don’t have time to maintain a dedicated server)
  5. all this will allow everyone in the family to add elements, it will need very little maintenance and it should also be fast
  6. an e-mail address will be provided to everyone (all serious providers give e-mail addresses)

Although I am running WordPress for this blog, although a friend of mine is running DotClear, I am tempted to try b2evolution (blog), TextPattern (blog and more) or even Vanilla (forum) for the first service (blog). What is interesting is that these tools are localized in French, they allow multiple author to write and, finally, they have an anti-spam service “out-of-the-box”.

For the second service (photo gallery), I am tempted to use either LinPHA, PhpWebGallery or singapore.

I’ll dig a little bit more for more information … I’ll try to finish all this before Monday.

A first scientific paper from the Falisse-Poirrier!

Nandini published her first paper in a scientific journal:

Falisse-Poirrier N., Ruelle V., Elmoualij B., Zorzi D., Pierard O., Heinen E., De Pauw E., Zorzi W. Advances in immunoproteomics for serological characterization of microbial antigens. J Microbiol Methods. 2006 Jul 3 (DOI access).

Congratulations! πŸ™‚

It is still in electronic format (ahead of print) but already available on the web (but not Open Access, unfortunately ; I think Nandini will auto-archive it somewhere). Here is Nandini’s BibTex entry (will be updated for volume and pages asap).

The "bioinformatic effort"

In the June 2006 issue of BioTechniques, Thomas Conrads and colleagues wrote an article about mass spectrometry used in biomarker discovery [1]. It is part of a “Special Section” devoted to mass spectrometry for proteomics analysis that is worth reading in itself. But one figure caught my attention. In this figure (reproduced below), they plot the mass spectrometry data acquisition effort and bioinformatic effort -vs- the experimental focus. In the few past years, people relied too much on the increasing power of mass spectrometry and bioinformatic tools in their experimental design. The authors criticise the fact that people “are overly dependent on technology and suffer from lack of imaginative sample preparation”. It’s not because analysis power is available downstream that sample collection and processing could be neglected.

Conrads'figure 1 about the importance of sample preparation
Reproduction of Conrads’figure 1

As shown in Figure 1, there is often an inverse relationship between the complexity of sample preparation and the amount of data acquired or the sophistication of the bioinformatic analysis. Simply put, minimal sample preparation prior to MS analysis will require more data acquisition and more sophisticated bioinformatic analysis. There is, however, a direct correlation between the amount of data acquired and the sophistication of the bioinformatic analysis.

Schematic protein identification process
Schematic protein identification process (for those who need it)

[1] T.P. Conrads, B.L. Hood and T.D. Veenstra. Sampling and analytical strategies for biomarker discovery using mass spectrometry. BioTechniques (June 2006) 40 (6): 799-805 (full text in html ; free registration required)