Open-Source on Jean-Etienne's blog

Start with a PyPortal in 2021

Sun, 04 Apr 2021 17:53:57 +0000

The Adafruit PyPortal is a great device, with a few bells an whistles already integrated in order to start small electronic projects (but expensive, ok ;-)). As usual, Adafruit wrote a nice introductory guide. But some parts are outdated. Therefore, here are a few steps to get you started with CircuitPython on a PyPortal in 2021 …

Digitize you charts with Engauge Digitizer

Fri, 04 Aug 2017 16:31:39 +0000

A few words of appreciation for an open source software that can help you a lot in your work, Engauge Digitizer (ED) from Mark Mitchell. ED is a simple, straightforward curve digitizer: it takes images with graphs like the one below and transform them (with a little help) in data you can use later on.

Fedora 23 on a Dell XPS13 (part 1)

Thu, 17 Dec 2015 21:05:40 +0000

Taking advantage of a trip to Canada and a very favourable CAN$:€ exchange rate, I bought a Dell XPS13 (9350 or “late 2015”), following excellent reviews from around the web. Dell sold a ’ developer edition’ of this laptop (shipping with Ubuntu Linux) but unfortunately it was out of stock on Dell US and I couldn’t find the item on the Dell Canada website. So I bought the Windows version with a touchscreen (it was Black Friday :-)).

Here is how to install Fedora 23 on it (and probably most other Linux distribution) … I will focus on three aspects (in brief: everything works out of the box, except the wireless card that needed some additional action):

How to boot and install Fedora Workstation
What works and what doesn’t work out of the box
Some things to do after installation (additional software)

Import PDFs and related metadata in Zotero

Thu, 03 Dec 2015 19:14:38 +0000

I discover new things everyday …

I wrote earlier that I really liked Zotero, a reference management software. However, there is one thing that was missing, imho: the capability to import PDFs (individually or in bulk) and correctly fill in the various fields of the reference.

But in fact, this already exists in Zotero! Just drag a PDF in the middle section (the reference list) then right-click on it and choose “Retrieve Metadata from PDF” (*). Retrieval of the title, the authors, the journal, etc. everything goes very fast and they are stored as a normal reference, now on the right.

Happy to use Zotero since a few weeks

Fri, 26 Jun 2015 19:33:24 +0000

For my work I need to reference a lot of statements, mainly with papers and books in the biological / medical literature. Usually “professionals” use two proprietary software, Reference Manager or EndNote (both owned by Thomson Reuters). But there are a few very interesting free alternatives (see this comparison of reference management software).

I switched from Mendeley to Zotero a few weeks ago and I’m very happy. Here is why …

How to write data from R to Excel (even if you don’t have Excel)

Tue, 21 May 2013 20:42:15 +0000

Following my previous posts on how to read/write Excel files from Matlab here is the way I use to read/write Excel files from R. Again it seems the Apache POI java library made developers’life easy. I use here the simple-yet-powerful xlsx package ( documentation here in PDF; project website).

Here you don’t need to install any additional files, installing the xlsx package from R does all the dirty work that for you. Then, reading an Excel file is very easy:

Map of GAVI eligible countries in R

Sun, 10 Feb 2013 22:48:45 +0000

I was trying to reproduce the map of the GAVI Alliance eligible countries (btw I was surprised India is eligible - but that’s the beauty of relying on numbers only and not assumptions) in R. This is the original map (there are 57 countries eligible):

I started to use the R package rworldmap because it seemed the most appropriate for this task. Everything went fine. Most of the time was spent converting the list of countries from plain English to plain “ISO3” code as required (ISO3 is in fact ISO 3166-1 alpha-3). I took my source from Wikipedia.

Android is catching up iOS

Fri, 21 Dec 2012 11:08:52 +0000

Well, there is nothing new in this statement. The smartphone OS Android is catching up and even overtaking its rival iOS in many domains:

more activated products per day and per year in 2011,
more Samsung Galaxy S3 (running Android) sold in Q3 2012 than iPhone4 and 5S (running iOS),
more devices worldwide,
catching up Apple’s market share in tablets,
…

All this is summarised in an infographics MBA Online designed (the original address is here: http://www.mbaonline.com/android/ - click at your own risk). It is sweet and colorful, with lots of numbers and some references in the end. Unfortunately these references are embedded in the image so you cannot click on them if you ever want to read more info.

How to write data from Matlab to Excel (especially when you don't have Excel)

Tue, 11 Dec 2012 13:09:50 +0000

If you are using Matlab on a MS-Windows PC with MS-Excel installed, there is no problem reading and writing data to Excel (in case your users/customers only understand this software but you still want to do the computations in Matlab). Here is the code to read (1st line) and write (2nd line):

[sourcecode language=“matlab”] inputs = xlsread(‘inputfile.xls’, ‘inData’, ‘A1:B3’); [writeStatus, writeMsg] = xlswrite(‘outputfile.xls’, myMatrix, ‘outData’, ‘A1’); [/sourcecode]

Now, there are several reasons why you may not be able to read and write directly to an Excel file: you have Matlab but

Android-based smartphones market share in Asia

Fri, 23 Nov 2012 23:01:57 +0000

31%

Tonight I was wondering what was Android market share in Asia. It is 31% according to a recent study from Ericsson’s ConsumerLab group ( reported by TechRepublic). Although dominant through most studied countries, Android is not dominant in Singapore (iOS has 46%), in Indonesia (RIM has 29%) nor in Vietnam (Symbian has 26%).

Last year ABI Research released a study where they showed that Android-based smartphones market share grew from 16% in 2010 to 52% in 2011 (but this included tablets and did not cover exactly the same countries as the Ericsson study). Voila :-)

Visualizing categorical data in mosaic with R

Tue, 15 May 2012 23:46:25 +0000

A few posts ago I wrote about my discomfort about stacked bar graphs and the fact I prefer to use simple table with gradients as background. My only regret then was that the table was built in a spreadsheet. I would have liked to keep the data as it is but also have a nice representation of these categorical data.

This evening I spent some time analysing results from a survey and took the opportunity to buid these representations in R.

Funny update of ql2400 and ql2500 devices in Fedora 14

Sat, 17 Sep 2011 22:21:03 +0000

[caption id=“attachment_1093” align=“aligncenter” width=“497” caption=“ql2400 and ql2500 update in Fedora 14”] [/caption]

Although some people think it’s a joke (see kalev’s comment on 2011-09-17 19:13:44 in the bugfix report), I won’t install this update; I agree it’s funny but refusing to install it at least gives me the feeling I have still something to say on my system (that’s also what free software are for, isn’t it?).

References, references, references!

Fri, 09 Sep 2011 00:09:00 +0000

When I studied biology as well as when I did my Ph.D., our professors were always after us because of references. I think with their precious help we learnt the art of referencing: choosing good references, citing them at the appropriate location in a text and, of course, giving enough information at the bottom of the text to allow the reader to find these references.

I just finished reading two articles in a recent edition of The Economist and they reminded me how important are these references. These articles are What would Jesus hack? and Worrying about wireless.

ForbidSleepingMode updated

Fri, 05 Aug 2011 21:10:34 +0000

Following some comments on the dependency to version 4 of the .Net framework, I rewrote ForbidSleepingMode in C++. You can open and compile the project with Qt (open source). The source code is of course updated. The mandatory screenshot as well :-)

As you can see, I took the opportunity to add a small field where you can specify your own interval at which the program will “tickle” your computer.

forbidSleepingMode

Tue, 19 Jul 2011 21:49:43 +0000

I just put my first small tool on GitHub: forbidSleepingMode. It will forbid your (Windows) computer to enter into sleep mode, acting as if there was activity all the time. I’m sure you can think of 1001 productive uses for such tool.

Technically, it just sends a “tickle” to the computer every 10 minutes forcing the display to remain on (hence: don’t set your screensaver to come before 10 minutes). Build it with Visual Studio 10 (I know, I know …).

Installing Fedora 14 on a Toshiba Satellite L670-10K

Wed, 10 Nov 2010 01:12:05 +0000

No issue, installation even smoother than the installation of Fedora 13 on the same machine, last month.

Installing Fedora 13 on a Toshiba Satellite L670-10K

Thu, 21 Oct 2010 23:31:15 +0000

I quickly needed a new laptop to continue working and I found a Toshiba Satellite L670-10K. It’s a nice entry-level laptop with a dual core processor (I didn’t know Intel was still doing Pentium-branded processors) and a 17" screen ( read the specs for other details). I downloaded the latest Fedora Linux (version 13, 64 bits ; and version 14 is coming soon) and installed it from the LiveCD. Nearly everything was recognized out-of-the-box: screen resolution, graphical card (Intel, with 3D effects), wired network, webcam, card reader, sound card, etc.

Sintel film released

Thu, 30 Sep 2010 21:17:14 +0000

After Elephants Dream and Big Buck Bunny, the Blender Foundation released Sintel. Technically, I think it’s superb. IMHO, the only negative point is, as for the two previous films, the story is rather minimal but it’s becoming better and better. But this doesn’t prevent me from enjoying watching it!

[youtube

&fs=1&hl=en_US]

Happy Software Freedom Day 2010!

Sat, 18 Sep 2010 21:29:56 +0000

Today, September 18th 2010, it’s Freedom Software Day all over the world. It is an annual worldwide celebration of Free Software, a public education effort with the aim of increasing awareness of Free Software and its virtues, and encouraging its use.

On the SFD website, there isn’t a lot of events registered for Belgium. There is only one, in fact, in Oostende ( LiLiT is doing an install party in Liege but I can’t see any reference to SFD; still, it’s a good initiative!). Well, a SFD on September 18th in Belgium might not have been a good idea if the goal is to increase awareness of Free Software: more than half of the population is celebrating the Walloon Region or preparing a Sunday without car in Brussels (while others are just looking for a government since April 2010!). So, at a personal level, I decided to give Ubuntu a try ( 10.04 LTS).

Bittorrent used to deploy updates

Tue, 20 Jul 2010 20:49:24 +0000

I just watched a video from Larry Gadea working at Twitter: Twitter - Murder Bittorrent Deploy System (speaking at CUSEC 2010).

Briefly, the problem Twitter was facing was the deployment of updates to thousands of servers in a short amount of time and dealing with errors (broken servers, e.g.). A nice, simple, cool and free way of solving this issue was to use the Bittorrent protocol (via Python and a stack of other free software) to actually deploy updates. In summary, you go from a unique repository facing thousands requests approximately at the same time:

FluTE makefile for wxDev-C++ (Windows)

Fri, 25 Jun 2010 01:27:57 +0000

FluTE is an influenza epidemic simulation model written by Dennis L. Chao at CSQUID. It works out-of-the box on GNU/Linux (just type make and run it).

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.

Welcome PDF comments in Evince!

Sat, 30 Jan 2010 22:52:24 +0000

Three months ago, I complained about the fact we can’t see comments made in PDF files in Evince. With a recent update to Fedora Core 12, Evince was also updated to version 2.28.2 and, among many improvements, comments ( annotations) added to PDF files are now visible :-)

Bye, bye, Adobe Acrobat Reader ;-)

Waiting for PDF comments in Evince

Sun, 11 Oct 2009 21:51:03 +0000

Evince defines itself as “simply a document viewer” (for Linux/Gnome and now for Windows too). However it can already read a lot of formats: PDF, TIFF, PS, DVI, DJvu and plans to support a lot more in the future.

But for me there is one important feature missing: the ability to read comments in PDF files. I sent PDF versions of draft documents to my PhD thesis promoters and they send them back with their comments. Open them in Evince: you’ll only get the balloons but no possibility to click on them (see Figure 1 below). Open them in Acrobat Reader and not only you can see that there are comments but you can also see their content (see Figure 2 below).

postr, simply puts your pictures on Flickr

Mon, 14 Sep 2009 21:26:53 +0000

I really like gthumb to have a look at my photos, quickly perform some basic modifications or effects and display all the photos to people around me. But there is one thing that is annoying me: it seems impossible for my gthumb version (2.10.11) to upload to Flickr, where I put some of my pictures. There is an " issue 73" in the GNOME’s GHOP Contest page from 2007 and the development seems to be done ; it’s just not yet in the main branch.

Wordpress problem with permalinks after upgrade

Mon, 10 Aug 2009 19:20:21 +0000

If you get error 404 with your permalinks and RSS feed after an upgrade of your Wordpress installation to version 2.8.3, it’s worth to check the “Permalinks” section (under the “Settings” tab in the admin panel). Try set it up to “Common”, save changes and then put it back to your previous structure (“Month and name” in my case). This should solve most of current 404 errors after upgrade. If not, check the Wordpress support forum.

Installing Pwytter on Fedora 11

Sat, 08 Aug 2009 10:12:38 +0000

This morning, it was impossible to post tweets on Twitter so I finally gave in to install a Twitter client. Amongst many software available, Pwytter seemed interesting to try: free software, written in Python were my two criteria.

Unfortunately, the installation process is not straightforward (although its use of the general python setup procedure). Here is how to install it on Fedora 11 from the command line:

Download Pwytter, unzip it, enter directory pwytter-0.8
Install ImageTK: as root, type " yum install python-imaging-tk" ( in Fedora, ImageTK was renamed python-imaging-tk)
Install simplejson: as root, type " yum install python-simplejson"
(optional) launch: python setup.py build
launch: python setup.py install
Complete the installation by copying some files with the 4 lines below (type them as root too) ( a comment in pwytter blog helps to solve the pwCache installation bug):

cp pwCache.py /usr/lib/python2.6/site-packages/pwytter-0.8-py2.6.egg
cp pwCache.pyc /usr/lib/python2.6/site-packages/pwytter-0.8-py2.6.egg
cp -r media/ /usr/lib/python2.6/site-packages/pwytter-0.8-py2.6.egg
cp -r theme/ /usr/lib/python2.6/site-packages/pwytter-0.8-py2.6.egg

Now you can launch pwytter from any user! In addition, since the source code is available and Identi.ca supports a Twitter-compatible API, let’s see if it’s easy to modify pwytter for Identi.ca :-)

A new home for IPGphor2reader

Thu, 02 Jul 2009 21:46:09 +0000

IPGphor2reader is a software meant to parse log (text) files resulting from an experiment with the IPGPhor and to plot graphs. I previously hosted it on my personal website and just moved it to Sourceforge, here. Amongst the various reasons for this move, I wanted the possibility for anyone to participate in the project and no hassle to manage this.

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

About file formats accepted by BioMed Central

Sat, 20 Jun 2009 21:32:48 +0000

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!

Fedora 11 is out (since a week or so)

Mon, 15 Jun 2009 00:19:54 +0000

This week, I nearly emptied my internet quota by downloading and seeding the new Fedora Core 11. For those who don’t know yet, Fedora is a Linux-based operating system that showcases the latest in free and open source software. What I particularly like in this GNU/Linux distribution is that its developers prefer to make changes to the original software instead of applying fixes specifically for Fedora ; in this way, all the other distributions may also take advantages of the improved software. You’ll find many reviews and " tours" on the web about this new Fedora. In the next paragraphs, I’ll just highlight some of the most interesting points I saw until now. Coming from a Fedora 9 also helps to pinpoint the major improvements (mainly from a user point-of-view).

Implication of Oracle buying Sun on Open Source projects?

Thu, 23 Apr 2009 22:40:34 +0000

Oracle and Sun announced a few days ago that Oracle will buy Sun. Others are more apt than me to comment on the financial and strategic impacts of this move (for example, in the Guardian, the New York Times, the Wall Street Journal or on Slashdot). I’m more interested in the potential implications this move could have on some Open Source projects which were backed by Sun. I indeed believe Oracle will continue the development of his contributions to Open Source software, whether they are notable ( Btrfs or Oracle Enterprise Linux) or less visible.

FOSDEM 2009, Gemvid video

Sun, 29 Mar 2009 23:05:23 +0000

Along with all the videos of all FOSDEM editions, the FOSDEM team put the 2009 videos on YouTube. So here is the video about Gemvid:

[youtube

&hl=en&fs=1]

The presentation in PDF is still available from the Gemvid webpage (and in live here).

Using Mantis with a reduced mail() function

Wed, 25 Feb 2009 21:42:40 +0000

Mantis is a free web-based bug tracker. As most web trackers, it uses e-mail to notify testers and developers about the evolutions of issues they have reported or they just follow. For that purpose, Mantis uses Codeworx PHP Mailer class that gives you the opportunity to use the PHP mail() function, sendmail or a SMTP server to send those e-mails.

The use of the PHP mail() function is the default option. Unfortunately, some web hosting companies limits the PHP mail() function by forbidding the use of the 4th and 5th (optional) parameters. The result is that you can’t use the e-mail functionality of PHP mailer / Mantis because they use the 4th parameter.

Fosdem 2009, February 7-8th

Sun, 11 Jan 2009 16:04:43 +0000

Fosdem is “a two-day event organized by volunteers to promote the widespread use of Free and Open Source software”. I will be presenting Gemvid during a lightning talk on Saturday :-)

Short script to add a timestamp on pictures

Sun, 23 Nov 2008 22:36:38 +0000

Here is a short script (1.6kb) to add a timestamp on all PNG pictures in a directory. It requires Python and the Python Image Library ( PIL). In order to use it, modify some parameters in the beginning to suit your needs (images directory, font file and size, etc.) and launch ./timestampFiles.py. Here is a before/after example (size of pictures is reduced to fit in this blog):

Taking automated screenshots from a live video camera

Sun, 23 Nov 2008 01:06:35 +0000

Following my previous post, I attached a video camera to the composite input of my tv tuner. One good thing I didn’t noticed yesterday is that mplayer can be told to directly use pvr:// as a source instead of the generic tv:// (with many options). So you just have to enter mplayer pvr:// -tv device=/dev/video1:input=0 in order to watch tv.

Noticed the input=0 above? This tells the tuner to take the video signal from the tv (read the mplayer man page to see how to change the channel). Now, since I connected my video camera to the composite video in, I need to tell mplayer to use it with input=1. One last thing: taking a screenshot in mplayer is done by pressing the ’s’ key (with option -vf screenshot. In summary, the image below was taken with mplayer pvr:// -tv device=/dev/video1:input=1:noaudio -vo x11 -vf screenshot (camera facing the screen).

A first step toward TV on my Linux laptop

Sat, 22 Nov 2008 00:31:05 +0000

I recently got a Hauppauge WinTV-PVR-USB2 (a TV tuner, video recorder and FM receiver) because I read it was well supported on GNU/Linux. The following post explains how I installed it on a Fedora Core 9. If you want to install it with another Linux distribution, some information may vary but most of the following steps will be exactly the same.

First connect the USB device, the list of USB devices shows my system has recognised it:

Watch your webcam with mplayer

Fri, 19 Sep 2008 23:01:24 +0000

A small post just to keep this command at hand:
mplayer -fps 30 -tv driver=v4l:width=640:height=480:device=/dev/video1 tv://

This allows you to watch what your webcam “sees” (provided it uses a video4linux webcam). Btw, Cheese is funny to use too!

I was also trying to find a decent Python library for video4linux but I only found outdated ones ( libfg, 2003, and pyv4l, 2002). I guess I’ll have to use some C library for a small project I’ll tell you about later ;-)

The "problem with TinyURL" is (partially) solved

Fri, 18 Jul 2008 19:30:48 +0000

Thanks to the free software project lilURL and one of its implementation at ur1, the problem with TinyURL is solved. Thanks Alexandre for the info. :-)

So now http://www.poirrier.be/~jean-etienne/ can be short ( http://ur1.ca/04d) and free at the same time: free to use, and free to look at source code.

Since I’m never fully satisfied (hmm, never say never), the next step would be an implementation of some “intelligence” in these short URLs (see Udi’s post). And since I never have time (or less and less), I’m a bit sad not to have that time to code a solution (which should be quite easy).

The problem with TinyURL ...

Sun, 13 Jul 2008 12:56:04 +0000

The problem with TinyURL.com is that its source code is not free. And I can’t find any other open services/projects that offers the same features (1).

I realized this when trying to add a long link in a Twitter update (2, 3). A maximum of 140 characters doesn’t allow you to add much text around. And it seems that a lot of Twitter users are using the TinyURL.com service which allows you to translate a small URL it gives you to the full, “regular” URL. For example, http://www.poirrier.be/~jean-etienne/ (37 characters) becomes http://tinyurl.com/6kq84z (25 characters).

AEL-NG?

Mon, 16 Jun 2008 23:00:14 +0000

A few days ago, I was sad to see that the Association Electronique Libre (AEL) website was down and only replaced by two measly tags. For those who didn’t know it:

The Association Electronique Libre is a belgian association protecting the fundamental rights in the information society.

The Association Electronique Libre supports the freedoms of speech, press, and association on the Internet and any electronical mediums, the right to use encryption software for private communication, the right to write software unimpeded by private monopolies, the right to access and preserve public domain and free digital information.
(from an old copy of the AEL website)

Alt+e, g, a

Sun, 01 Jun 2008 16:38:31 +0000

This is the “shortcut” sequence of keys in order to get the list of changes in a text document in OpenOffice.org. It works very nicely with MS-Word documents, a useful feature when you are obliged to exchange work with colleagues, mentors, etc. who only use the proprietary word processor.

IMHO, the only problem is the way the list of changes is shown to the end-user in OpenOffice.org: as in other word processor software, changes are underlined in a different color for each contributor and a small hint tells you what happened to the hovered block of text, who did it and when; unlike other word processors, you can’t accept/refuse any change by right-clicking on it (you have to do it from the separate window). I do not find this intuitive and, sometimes, annoying …

GNU tools on MS-Windows

Sun, 27 Apr 2008 20:42:27 +0000

When you are used to work on a computer with GNU/Linux and are obliged to process your files on a MS-Windows system for some time, the GnuWin32 project can come in handy. They provide a lot of command-line tools from the GNU collection (sed, iconv, tar, bzip2, … see the whole list of packages they provide).

This evening, I needed to convert a lot of files from UTF-8 to iso-8859-1 (because it seems no decent Windows text editor can correctly translate text between these two encodings). Apparently, the GnuWin32 project removed the recode tool. But it can be easily replaced by iconv. With iconv, it’s done with:

Two nice schemes about Open Source

Sun, 13 Apr 2008 22:04:22 +0000

I don’t know how I stumble upon this report of a conference ( English translation) from Avi Alkalay but I liked 2 schemes he showed.

In this first scheme (left), I like the way it reminds you that “Open” is not only about software, source code. But now that more and more people are aware of the benefits of Open Source software, it’s interesting to also stress the other sides of openness: open standards (like OpenDocument), open hardware, open architecture.
In the second scheme (below) is about the trend from private control / closed access to public control / open access (apparently from Rebecca Henderson; it could be interesting to find this whole presentation from 2004).

One more Open Source software at ULg

Wed, 28 Nov 2007 20:47:29 +0000

After the promotion of Open Access (see Bernard Rentier’s blog) and a history of publications in Open Access journals (see this last article from the Cyclotron Research Center in PLoS), the University of Liege is slowly slowly publishing Open Source software too.

The last free software published is exams, an assessment management system (for on-line exams, …). They chose the GNU GPL 2, apparently without the possibility to upgrade to version 3 (I don’t know if it’s deliberate or not). And you can download the source code here.

Vertical badge

Wed, 07 Nov 2007 20:13:48 +0000

I was writing the next version of my badge counting the number of days without Belgian government when Laurent added his comment requesting for a vertical version. You can see it on the right.

Since the original release, I also added translation of the sentence in Dutch and German (after all, Belgians are speaking 3 official languages). And I approximately centered the text on the vertical version (I personally prefer the text on the right for the horizontal version but you can easily modify this by yourself).

How many days without governement?

Tue, 06 Nov 2007 00:00:37 +0000

Now it’s not a secret anymore: more than 148 days passed since we, Belgians, went to vote (it was on the 10th of June 2007) and we still don’t have any government!

If you want to count the numbers of days without Belgian government, it’s easy: just have a look at Belgian newspapers. Or … have a look at the counter below (in French, Vlaams or German) ;-)

More on Java DBs comparison

Mon, 17 Sep 2007 00:43:32 +0000

Following a comment from Alexandre on a previous post, I went a little bit further with my performance test of database engines running under Java. This evening, I tested a profiling tool and a variable number of insertions/retrievals (I didn’t tested transaction).

Taking the code from the previous time, I simply changed the number of elements to be inserted/retrieved. As expected, the durations of object initialization (except for 2 points for Derby and H2) and database creation did not change with the number of elements to be inserted, Derby being still the slowest engine to create a simple database (1 table only). The durations of the insertion step increased slowly with all the database engine, except for SQLite+JDBC: you can see a much steeper initial angle in the increase of the duration in the graph below (be careful: x-axis shows logarithmic values).

SQLite+JDBC, worst than Derby!

Wed, 05 Sep 2007 23:39:46 +0000

Following a comment from Alexandre on a previous post, I included SQLite in my performance test of database engines running under Java.

What prevented me from using SQLite in the previous test is that it’s not a pure Java database and one have to use third-party JDBC driver and implementation classes in order to manage this database engine. IMHO, I also dislike another fact: SQLite does not enforce data type constraints ( and it’s a feature, not a bug) so everything is stored as ASCII string, even if you have very few other “artificial” data types.

Why did Sun chose Derby?

Tue, 04 Sep 2007 23:44:44 +0000

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):

Do your laptop fans produce a lot of noise?

Sat, 28 Jul 2007 21:41:37 +0000

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):

OPML output in catrss

Sat, 28 Jul 2007 20:41:55 +0000

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.

Picklist Editor 0.2

Sat, 28 Jul 2007 02:08:45 +0000

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 :-)

Picklist Editor 0.1

Thu, 26 Jul 2007 15:36:41 +0000

When you work with 2D gel electrophoresis in proteomics, you end dealing with “pick lists”. For this purpose, I wrote Picklist Editor, a tool to help visualize and modify this pick list.

As usual, software and source code are available here. Feel free to use it and report any bug or your wish list :-)

(and if you didn’t understand everything above because you are not in the proteomics field, just go to the page too because I also wrote a small introduction)

catrss 0.1

Tue, 24 Jul 2007 04:58:17 +0000

One day, one has to sit at his/her table and try to really understand how to deal with XML. Since I think I can only learn with a project in mind, I took Alexandre Dulaunoy’s mergerss suggestion and tried to develop my own catrss.

As the name implies, catrss is one of the many descendants of the cat command. Catrss is used to concatenate RSS file(s) to standard output. In its most simple form, you simply have to give it some RSS files to parse and it will concatenate them for you ; the command is:

oncolour - a Flickr add-on for background

Mon, 23 Jul 2007 01:45:10 +0000

After discovering the Flickr API, I started coding oncolour this night and here is the result … oncolour is a PHP script that allows you to display your photos from Flickr on your own website and with a specific background colour. It’s better with an example … This URL " http://www.epot.org/flickr/oncolour.php?id=860125589," will give this result:

Some other solutions have been developed and used ( example) but this one is really free:

free for use (see here how to use it - even for your photos - and a description of all the options) and
free to re-use (see here how to download the script and use it on your own server).

Feel free to use it! :-)

GeoPolis - watching the watchdogs

Fri, 20 Jul 2007 01:36:39 +0000

Quuxlabs is releasing the alpha version of GeoPolis, a web service to gather and show the ongoing police control. More info can be found on the project website and on the Quuxlabs blog. I made some comments regarding the service accuracy, automation, security and independence but I’ll be glad to use the service once I’ll be able to drive again.

Btw, in the same topic – watching the watchdogs, my map of cameras in Liege (see announcement and update) is now located on the CCLV website. The database management is also handed over to them. Moreover Christophe Cattelain is now systematically taking photos of those cameras in Liege and he publishes them on Flickr …

Miro ...

Wed, 18 Jul 2007 16:43:45 +0000

It’s so boring to lay down the whole day (sprain at left ankle), I decided to give a try to Miro, a software to “watch internet video channels as easy as to watch TV”. Before trying it, I tried to watch their video demonstration but it’s not working since it requires the proprietary Flash player …

Now, if you want to try Miro, do not use “yum install Democracy” on Fedora 7 (Democracy Player is Miro former name). It will give you version 0.9.5.1-10 that will cause many problem (the main one being it won’t run).

Introduction aux Logiciels Libres

Fri, 29 Jun 2007 00:11:22 +0000

AprÃ¨s ma prÃ©sentation d’hier Ã la soirÃ©e du Liege Linux Team, j’ai placÃ© ma prÃ©sentation en ligne : " Introduction aux Logiciels Libres" (ou directement : fichier PDF, 1.8Mo). Tout commentaire ou amÃ©lioration possible est le(la) bienvenu(e) !

Edit (a little bit later): since I usually write in English here, I translated my presentation in English. It’s here: " Introduction to Free Software" (PDF, 1.9Mb).

June 28th: Intro to free software conference

Thu, 21 Jun 2007 21:44:46 +0000

On June 28th evening, the Liege Linux Team is organizing a conference to introduce free software. Three topics are scheduled: an introduction, a presentation of free software related to internet and a presentation of “offline” free software. They already left some time for discussion (between and after the talks). It will take place here (Auditoire Grand Physique, 1st floor), in the city center.

Englarge the image - Poster in PDF

Please note talks will be held in French but feel free to come and talk in English: nearly everyone understand English

Stupid EULA!

Fri, 08 Jun 2007 11:40:53 +0000

/. has some interesting comments about a story of a man who is suing PC manufacturer Gateway. He alledges Gateway wouldn’t fix a broken machine he bought, replace it nor refund his money. But the most interesting part is that Gateway doesn’t agree to be sued in court because an arbitration clause in their End User License Agreement (EULA) “require a dispute to be settled in private forums chosen by companies instead of in public courtrooms” (the man stated he can’t read the EULA since “the computer’s graphics were so scattered he couldn’t read the box of terms and conditions or click the Accept button”).

When business got things right about Free/Open Source licenses

Mon, 28 May 2007 14:49:49 +0000

It’s always interesting to see “business” people getting things right about the Free/Open Source world. For example, the last month Boulder Open Coffee Club was dedicated to “open source issues that developers face”. The NVA blog contains a summary of the recommendations. Basically, it is: " know the licenses you are using and what you can(’t) do with them". And AskTheVC gives links to Lawrence Rosen’s book: " Open Source Licensing" (not read yet, maybe for a future post). They also link to a Boulder’s company ( Openlogic) that helps you to maximize returns, minimize risks and accelerate innovation with Open Source (all keywords you should have in a business plan! ;-)). They also have some resources about Open Source for businesses.

Disappointed by BSN meeting

Mon, 07 May 2007 22:38:58 +0000

I’m very disappointed by this BSN meeting. This event is organised every 2 years so you might expect some quality standards. Well, don’t expect too much … (don’t expect anything, in fact).

Morning talks were ok, nothing more: it was not better nor worse than any other congress. But the poster session was not organised at all and there was no support from senior scientists … Moreover, authors of about 1/3 of posters didn’t even deign to come and hang a poster! Most of senior scientists left before the afternoon poster sessions (usually, questions from seniors are more useful than other students’ questions); maybe 2-3 seniors were left (for the whole Belgium!!!). And the final touch, lunch was not free (not even sandwiches!) although we paid 45€ for registration (free for members - membership is 12€ per year for students). Instead we were redirected to the UAntwerp canteen … Are they not smart enough to find a sponsor? I think it would have been better to attend the Neuroinformatics Meeting only.

Conversion of address book from SquirrelMail to Yahoo!Mail

Fri, 20 Apr 2007 19:45:58 +0000

In case someone will need it, here is a very small Python script that will convert your address book from SquirrelMail to a file you can import in a Yahoo!Mail address book: addressbookS2Y.py (2ko).

To use it:

save the “program” in the same directory as your address book you imported from SquirrelMail
rename your address book from SquirrelMail as “addressbook1.csv”
download and install Python (if not already installed)
launch the “program”

VoilÃ ! You have now a file named “addressbook2.csv” that is suitable for Yahoo :-)

Mapping cameras in Liege

Wed, 18 Apr 2007 00:26:42 +0000

A lot of publicity is made around CCTV cameras in London (e.g. recently). But surveillance cameras are also invading other cities like Liege. You can be pro or against. The least thing is awareness: citizen should know where they are and how data is used. But nor the Liege city, nor the Liege police websites display a map of cameras. So I decided to create such a map here (in French). Of course, I cannot do everything by myself. If you know the location of some camera, just let me know and I will add them on the map.

Mapping my ride

Sat, 14 Apr 2007 23:20:44 +0000

Nearly 2 months ago, I got a GPS tracker. I discovered its antenna is sufficiently sensitive to work in my pocket so I took it on my Saturday morning bike ride. Back home, I was able to retrieve data from the tracker in various formats. What can I do with this data? Find the total distance I rode, of course!

I am lazy ;-) so I decided to use the Kompass track file since it’s only a CSV text file (I should have used the GPX file format but parsing XML is still more difficult for me than a plain text file). With a rather simple Python script, I was able to store all the latitudes and longitudes in a collection of objects. But, hey, how do I compute the distance from longitudes and latitudes?

Open source animal behaviour monitoring

Fri, 06 Apr 2007 22:25:32 +0000

In the last issue of the Journal of Neuroscience Methods (impact factor: 1.5), 3 papers deal with animal behaviour monitoring and 2 of them introduce open source software.

Roseanna Ramazani and her colleagues “designed an automated system for the collection and analysis of locomotor behavior data, using the IEEE 1394 acquisition program dvgrab, the image toolkit ImageMagick and the programming language Perl” [1]. What is interesting is that they highlight the longevity and reliability of open source software, leaving behing the simplistic view “open source = free as in free beer”:

How do I handle my bibliographic data?

Fri, 09 Mar 2007 05:38:27 +0000

In science, you have to justify nearly all your assertions and this is done by citing another scientific paper, called a “reference”. With practise and advices of some people, I arrived to a satisfactory references management system I’ll explain below. My “problem” is that in the academic world where I work nearly everyone use EndNote or Reference Manager, two proprietary reference management software for MS-Windows. And I want to use the simple yet powerful BibTeX system.

Sunday @ Fosdem

Sun, 25 Feb 2007 19:06:30 +0000

This Sunday, I attended only two talks. These talks were in the embedded track since I was with my brother who is interested in this. The first talk, “SH-2A Linux kernel” by Yoshinori Sato, was very difficult to follow since Yoshinori did not tell us what is the SH-2A microprocessor (it is apparently used in cars, a.o.) and his English was very bad. In the second talk, Vitaly Wool introduced XIP, a way to directly run portions of software from where it’s stored in a type of Flash memory (instead of being copied to RAM first). With XIP, you can reduce boot time (or at least the “time to splashscreen”, especially interesting in handheld devices where you want to quickly be “productive”). But you can have other occasions where speed of execution is more important than price (because the type of Flash memory used is more expensive than standard RAM). Yesterday, Jim Gettys said the OLPC laptop can boot very quickly but it was thanks to the use of LinuxBIOS (and maybe XIP?). I also liked when he took a pen to show us something on a slide and said that it’s “because my wife is here and she said it’s bad manners when I point at things with my finger”. ;-)

First trace for OpenStreetMap

Sat, 24 Feb 2007 22:41:26 +0000

OpenStreetMap is a “project aimed squarely at creating and providing free geographic data such as street maps to anyone who wants them. The project was started because most maps you think of as free actually have legal or technical restrictions on their use, holding back people from using them in creative, productive or unexpected ways.” I thought it was worth participating and more documented than the UPCT project. So I got a Locosys NaviGPS GT-11 and used it for the first time on the way to FOSDEM (and back). I did a small mistake by taking an interval between points of 30s: on a highway, at 120km/h, 30s means 1km and the road direction can change a lot. When I’ll have more time, the next step will be to do some edition and mark roads, highways, interesting landmarks, etc. Stay tuned …

Saturday @ Fosdem

Sat, 24 Feb 2007 22:10:12 +0000

I spent this Saturday at FOSDEM, listening to some interesting talks.

Pieter Hintjens spoke about the Status of Software Patents in Europe. As the FFII president, he should clearly be against software patents. But, although his speech went in this direction, the 3 new FFII initiatives are diluting his/its position as well as the threat (the 3 initiatives are European patent conferences, the creation of the European Software Market Association to lobby the EU and a Campaign for Ethical Patents). Let’s talk seriously: software patents are not a solution and shouldn’t be allowed ; no trade-off.

GUI version of pyP2B

Thu, 15 Feb 2007 23:08:29 +0000

My python script pyP2B was command-line only. Tonight, I played for the first time with Tk, re-wrote pyP2B as a class and thus added a GUI.

Its webpage is updated ; the archive containing both command-line and GUI versions is here: pyP2B.tar.gz (3kb).

I give up!

Tue, 13 Feb 2007 00:44:10 +0000

OK, I am giving up the Jadoo project. It could have been a very interesting project. But if I don’t give up now, it will stay in my mind and prevent me from starting new projects or continuing more important projects. But it’s a temporary giving up: who knows how much time I’ll have in 2 or 3 months.

For those interested in Jadoo, here is the short story: everything started with a post on Alexandre Dulaunoy’s blog, then I tried a first version and finally I wrote a small update. Files are still here: jadwrite.py and jadpub.py.

Some news about Jadoo

Tue, 02 Jan 2007 03:13:45 +0000

Here are some news about the Jadoo blog engine …

I updated the CSS file (2ko) and corrected some mistakes; now, all HTML/CSS tags are correctly used.
I updated the main script in order to link to Technocrati for all tags
I also updated the footer (= the side bar in the published page); it now includes the Technocrati search box
I added the blogroll. It’s not showing links in random order like many other blog engines. But do we need that feature?

Some tasks still need to be done:

Easy backup @ ULg

Wed, 27 Dec 2006 23:12:17 +0000

While reading the GnomeFr planet, I found this nice article to save documents on my university backup system (written by Steve Frécinaux).

First tryout of Jadoo

Thu, 14 Dec 2006 02:10:32 +0000

This is my first post with the Jadoo blog engine. As I stated before, I was planning to write my own blog software with these goals:

Simplicity
No PHP nor any script for the client
All the processing done un Python, offline
No DB
(maybe some other goals but I don’t remember them, right now)

I’ll try to apply the “release soon, release often” principle (where does it came from?): before writing an entry, launch jadwrite.py ; to create html files, launch jadpub.py ; then upload html files with your FTP client (scripts are highly customized for my blog, for the moment ; and everything doesn’t respect all the standards). I’ll also to retrieve all my previous posts (but the URL will be changed ; the RSS URL also changed). But for the moment, I have other important work to do … There is no system for comments for the moment (I don’t know if there will be one in the future) but you can send me comments and requests to jepoirrier@gmail.com.

Plugins for Digital Object Identifier lookup

Fri, 17 Nov 2006 22:29:52 +0000

I’ve just written some “search plugins” for Firefox (1.x and 2.x) that allow you to quickly look for a specific Digital Object Identifier ( DOI). These DOI are more and more used in biomedical sciences. One of their interesting features is that they allow direct linking to the scientific article.

The plugins are availble here. If you already have Firefox 2, the installation procedure is very easy: all you have to do is go to the plugins page, click on the small arrow near your Firefox search box and choose the “Add DOI lookup” option; it will then automatically be installed for you.

OSS/FS players about GPL Java

Tue, 14 Nov 2006 23:52:17 +0000

Sun opened Java in the most elegant way of doing it (imho): the licence is the GPL. This move was analysed and commented by many people. Even some important Open Source/Free Software players gave their comments on a Sun website. Unfortunately, their comments are only available in a proprietary video format.

You can now have access to audio recordings of these interviews ( Brian Behlendorf, Paul Cormier, Eben Moglen, Tim O’Reilly, Mark Shuttleworth, Richard Stallman and Dr. Marcelo K. Zuffo), to a text transcript and even to SHA1 sums of the audio files!

Simple Sitemap.xml builder

Sun, 05 Nov 2006 23:40:45 +0000

In a recent post, Alexandre wrote about web indexing and pointed to a nice tool for webmaster: the sitemap. The Sitemap Protocol “allows you to inform search engines about URLs on your websites that are available for crawling” (since it’s a Google creation, it seems that only Google is using it, according to Alexandre).

If you have a shell access to your webserver and Python on it, Google has a nice Python script to automatically create your sitemap.

Automated Pubmed reference to BibTeX

Sun, 22 Oct 2006 21:44:15 +0000

In biology, we often need to use PubMed, a biomedical articles search engine for citations from MEDLINE and other life science journals.

In the MS-Windows world, you have nice, proprietary tools (like Reference Manager or Endnote) that retrieves citations from PubMed, store them in a database and allow you to use them in proprietary word processing software (in fact, in MS-Word only since nor Wordperfect nor OpenOffice.org are supported). If you are using BibTeX (for LaTeX) as your citations repository, there isn’t a lot of tools. The best one, imho, is JabRef, a free reference manager written in Java (for me, the only “problem” is that it adds custom, non-BibTeX tags). Or you can edit the BibTeX file by yourself with any text editor.

Playing with Python and Gadfly

Sun, 01 Oct 2006 17:53:59 +0000

Following my previous post where I retrieved EXIF tags from photos posted on Flickr, here is the next step: my script now stores data in a database.

There is a lot of free wrappers for databases in Python. Although I first thought of using pysqlite (because I am already using SQLite in another project), I decided to use Gadfly, a real SQL relational database system entirely written in Python. It does not need a separate server, it complies with the Python DBAPI (allowing easy changes of DB system) and it’s free.

Playing with Python, EXIF tags and Flickr API

Sun, 01 Oct 2006 03:16:09 +0000

Some days ago, I was quite amused by Flagrant Disregard Top Digital Cameras: these people daily took 10000 photos that were uploaded on Flickr and looked at the camera makes and models of these photos. This kind of study is interesting because one can see what people are actually using and what camera models can give good results (with a good photographer, of course). I was just disappointed by the fact that they are not saying anything about their sampling method nor the statistics they can apply to their data. I then thought that I can do a kind of survey like this one and publish results along with the method.

"A closed mind about an open world"

Wed, 09 Aug 2006 23:26:01 +0000

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.

Screen recording software for GNU/Linux

Wed, 09 Aug 2006 00:06:42 +0000

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).

Release of IPGPhor2Reader

Sun, 14 May 2006 01:45:13 +0000

IPGPhor is a device from GE Healthcare (formerly Amersham Biosciences) that performs an isoelectrofocusing of proteins. Version 2 of IPGPhor can be connected to any computer via a serial cable. GE Healthcare provides a monitoring software but no post-hoc analysis software. This gap is efficiently filled by IPGPhor 2 Reader.

Today, I wrote “IPGPhor 2 Reader”. Its goal is to parse log (text) files resulting from an experiment with the IPGPhor and to plot graphs. This software (for MS-Windows, since IPGPhor logs are collected on a MS-Windows computer) is available here.

Goodiff monitors (changes in legal documents of) service providers

Mon, 27 Mar 2006 23:29:37 +0000

GooDiff began its work a week ago and I didn’t see much news/blog posts about it. If I correctly understood, the idea behind GooDiff is to monitor changes in legal documents of (internet) service providers (like Google or Yahoo!). Indeed, service providers are often trying to change on the fly their legal documents, especially in some critical sections like privacy, copyright and alike. With GooDiff, consumers and users are now able to keep track of these changes. Thanks Alexandre!

Présentations "Messagerie instantanée" et "OOo Impress" aux Namur Linux Days 2006

Sun, 19 Mar 2006 00:42:23 +0000

Les Namur Linux Days avaient pour objectifs de prÃ©senter les applications libres, sous GNU/Linux et disponibles pour l’utilisateur final, leur degrÃ© d’utilisabilitÃ©, leur Ã©tat d’avancement et leur diversitÃ©.

Ma premiÃ¨re prÃ©sentation Ã©tait consacrÃ©e Ã la messagerie instantanÃ©e sous GNU/Linux (dont Jabber !) et vous pouvez la tÃ©lÃ©charger ici (page reprenant toute une sÃ©rie d’informations dont la prÃ©sentation en PDF).

Ma seconde prÃ©sentation Ã©tait consacrÃ©e Ã OpenOffice.org Impress. Cette page reprend plus d’informations ainsi que la prÃ©sentation Ã tÃ©lÃ©charger.

Why bother with denunciations? Just use free software!

Wed, 01 Mar 2006 21:28:06 +0000

I really had a hard day at work, moving my desk from one room to another one and coping with unexpected problems. But I finally found some time to look for a new graphic card for my desktop PC (btw. the OpenGraphics project released the schematic of its first FPGA). While reading an article on Tom’s Hardware, I saw a flash animation for the BSA that explicitely ask for denouncement about software without licence. It was so farcical I captured the animation and added a small message at the end. You can download the AVI file here (.avi, 2Mo).

LiLiT was also at FOSDEM 2006

Tue, 28 Feb 2006 21:47:51 +0000

From the LiLiT homepage: Breaking news!!

Richard Stallman’s visionary statement at Fosdem 2006 : " Even HURD is history. You should now use GNU/Tchantchux!". For those who don’t already know it, Tchantches is a mythical character from Liege (see Liege’s folklore) and Tchantchux is a mix between Tchantches and Tux, the Linux mascot.

You can see the complete photo coverage here ;-)

Namur Linux Days 2006: March 18-19th

Mon, 27 Feb 2006 00:53:47 +0000

On the 18th and 19th of March, 2006, the Namur LUG will organise the " Namur Linux Days 2006". Despite an English title and this post in English, all the talks will be held in French.

On the 18th (Saturday), there will be two main keynotes: an introduction to Free Software by Maxime Morge and a presentation about intellectual property and free software by Philippe Laurent. Between these two keynotes, there will be a lot of talks about office, multimedia and internet free software for the general public. I will give a talk about OpenOffice.org Impress. The complete schedule is here.

Some thoughts on Saturday session at FOSDEM 2006

Mon, 27 Feb 2006 00:29:28 +0000

I went to FOSDEM 2006 on Saturday 25th ( schedule here). This year, I went with my brother Laurent (as usual) and my wife, Nandini. This was the first time at FOSDEM for her, it was also the first time she saw so many geeks and I am not sure she enjoyed her day…

In the morning, after a small introduction, Richard M. Stallmann gave his keynote on software patents. Of course, he was preaching to a converted audience (i.e. everyone is against software patents). And, even if we didn’t learned new information on what’s going on, it is always interesting to hear someone else’s opinion (event if it’s the same opinion as us) and a formal presentation on the subject. Two things turned Nandini against Richard Stallman… At one moment, RMS rudely asked that someone “removes this source of noise” (talking about a baby making some noise). Then, during the question, RMS roughly replied to someone trying to ask his questions because he was not talking louder enough (from the middle of the assistance) and because he “dared” to use the words “Open Source” in from of “Him”. I must say that she’s right: we seemed to easily forgive his behaviour because we know the character. But, imho, you can still be a great man, father of the GNU project and be polite.

The wonderful "I'm feeling lucky" button from Google ... (hem)

Thu, 19 Jan 2006 01:33:59 +0000

The sixth Free and Open source Software Developers’ European Meeting ( FOSDEM) is a 2 days event, organized by volunteers, to promote the widespread use of Free and Open Source software. It will take place in Bruxelles (Belgium) on the 25th and 26th of February 2006.

On their promotional material page, they give some links to website that already display their banners. One of them refers to a “belgian LaTeX reference site”. Instead of the correct URL, they did a small mistake (at least at this time ; I’ve sent an e-mail for the correction) and they wrote http://http//www.latex.be.tf/ (don’t use this yet). I didn’t noticed the difference because the wrong URL is “hidden” by the text “LaTeX” (as any other regular link on the internet). Now, click on the wrong link and you’ll be redirected to the Microsoft website if you are using Mozilla Firefox. Why?

First presentation with LaTeX Beamer: RFT in fMRI

Wed, 11 Jan 2006 01:01:24 +0000

Today at 11:00, I’ll be doing my first real presentation with the LaTeX Beamer class. It will be about Random Field Theory in functional imaging (fMRI), a topic I’ve never done, ever, in my life (I am working on other techniques in the same lab). But, anyway, preparing this presentation was a good challenge (to understand a new technique from scratch and to do it with Beamer). I am quite impressed with Beamer ease of use.

Firefox dans le journal "Le Monde"

Thu, 01 Dec 2005 09:49:25 +0000

(For once, this post will be in French since I am refering to a French newspaper)

Dans son article intitulÃ© " Firefox souffle 18 bougies et poursuit sa mue", Eric NunÃ¨s parle de la sortie de Firefox 1.5, de ses parts de marchÃ© (notamment face aux autres navigateurs), de la fondation Mozilla Europe et du projet de loi franÃ§ais interdisant tout systÃ¨me de diffusion de connaissance n’intÃ©grant pas un procÃ©dÃ© technique de traÃ§age de l’utilisation privÃ©e (HTTP, FTP, SSH, etc. ; certains diront que c’est la fin des logiciels libres, d’autres que c’est la fin d’internet …).

LaTeX Beamer

Tue, 22 Nov 2005 11:48:54 +0000

Since I had some time during lunch, I discovered the LaTeX Beamer class. I’ve put what I did here.

Can you trust entertainment and computer-security companies?

Thu, 17 Nov 2005 23:54:59 +0000

In an interesting article on Wired, Bruce Schneier is showing the collusion between computer-security companies and an entertainment corporation.

Sony BMG Music Entertainment distributed a copy-protection scheme with music CDs that secretly installed a rootkit on your computers. A rootkit is a software usually used by an intruder after gaining access to your computer and in order to steal information, track your habits, collect your preferences without your knowledge nor your consent. Moreover, you can’t remove it since it will damage your operating system (the main software of your computer).

Automate the creation of graphs with Graphviz

Tue, 16 Aug 2005 08:01:25 +0000

“Automate the creation of graphs with Graphviz” is my first article for the LinuxFocus magazine. You can read it in English and en franÃ§ais : “Automatiser la crÃ©ation de graphiques avec Graphviz”. Have a nice reading! :-)

Now, I’ll continue to translate some articles from English to French. If I find another interesting software, I’ll write another article.

Mplayer install for FC3

Tue, 09 Aug 2005 10:00:42 +0000

I had a problem with the default video player in the Fedora Core 3, Totem (it couldn’t initialize a Gstream object or something like that). Instead of fixing it, I decided to install MPlayer and I discovered two interesting websites:

GnomeFiles, a GTK+ (Gnome) software repository
Grey Sector, a RPM software repository that also has the RPMs for MPlayer with codecs, skins, etc.

While we are talking about MPlayer, they need a new server: if you have some money to spend, please participate. And, about Gnome, the new issue of the Gnome Journal is out …

When open source software teaching meets biology

Fri, 29 Jul 2005 13:28:03 +0000

Open source software are more and more observed (if not used) in the biological sciences field. They provide all the advantages of Open Source software, plus they bring needs for consensus on file formats, data representation and manipulation methods. I’ve just read a short article from Greg Wilson ( in Nature) who is working with the Python Software Foundation “to develop a course that will teach scientists and engineers the 10% of software engineering they need to solve 90% of their problems”. Their goal is to “introduce them to some open-source tools and working practices that can reduce the amount of time they spend programming by up to 25%”. The course is already available here ( Software Carpentry) … for free, of course!