Projects 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 But some parts are outdated.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 …

Programming Merit Badge presentation (2020)

Sun, 02 Feb 2020 04:29:08 +0000

This year, my elder son graduated from Cub Scouts to Scouts (time flies very fast!) and I signed up to be a counselor for Programming (and Public Health) in his troop.

Today, February 1st, 2020, was Merit Badge Day and I taught 6 scouts what is programming and the basics of programming in Python (and Scratch - but they all knew that already) (and nobody chose Public Health …).

I am now sharing my presentation and a few tips and tricks. Feel free to re-use, improve and give me any feedback to make it better.

Jadoo and static website generators

Wed, 18 Nov 2015 19:03:10 +0000

Coming back from holidays, I fired my RSS reader and, among many interesting posts, I found this one from Smashing Magazine about static website generators being the Next Big Thing on the web (and a follow-up deep-diving into four of them).

The first paper describes how the web started as something static, became all dynamic and is progressively coming back to something more static, at least for some specific tasks. The interesting thing is that the author also describes pros and cons of each stage and why the web jumped to the next level.

Idea shared #2 - the feedback toothbrush

Mon, 22 Oct 2012 21:26:28 +0000

After the T-shirt that measures your sleep better than an app, here is idea #2: the toothbrush that provides some feedback.

The idea is simple - so simple it was already applied elsewhere. The idea is to provide feedback about the quality of the way people brush their teeth. The Brushduino focuses on entertaining kids to keep them brushing at the right place for the right amount of time. Other projects (with many variants) focus specifically on time spent brushing.

Idea shared #1 - measure your sleep

Sat, 22 Sep 2012 21:48:32 +0000

I don’t consider having more or better ideas than others. But I gradually realized I have less and less time for some activities like programming, electronics etc. Maybe that’s how we realize we are getting older now adults. So I decided to share these ideas rather than fueling the illusory idea that I will implement them one day.

So idea 1 is about measuring sleep. I recorded animals’sleep during my Ph.D. - but it was thanks to an EEG device. I think that if you want to understand or improve something you have to first measure it in a way or another. So I started to try to measure my own sleep with an app ( Sleep Cycle). But despite its good reviews it doesn’t work, at least for me.

Maximum number of characters in a Windows path is 260 characters

Tue, 28 Feb 2012 18:35:30 +0000

A Java project compilation went berserk and I ended up with a directory structure of more than 260 characters. I stopped the mad process but it already created more than 50 successive duo of path “build/classes” …

Now I had to delete this structure. And, to my surprise, it was impossible. When you try to just press the “Delete” key with the root directory selected in the File Explorer, you get a Path Too Long exception. The reason is that the maximum length of a path according to the Windows API (MAX_PATH variable) is defined as 260 characters. I tried some other methods but all of them failed:

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 …).

Tetris wall

Tue, 20 Jul 2010 21:59:34 +0000

Dear wife,

I agree to have the decoration you want everywhere in our new home. You can have all the furniture and appliances you want in the kitchen. I’m OK if all the shelves with my computer books are in the basement. OK too if you don’t want to see the file server in the living room. Agreed: I’ll put back Windows on your laptop. But …

But I absolutely want one wall painted like these:

Evolution of H1N1

Fri, 23 Oct 2009 23:16:11 +0000

I needed some data to test the pChart charting library so I decided to use WHO data about swine flu (in its weekly updates). The only issue I had was that the WHO started to collect data by country and changed to gather data by regional offices from July 27th, 2009 onwards. So graphs below are only by regional offices.

For your information:

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.

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).

FOSDEM 2009 and Gemvid 0.6c

Sun, 08 Feb 2009 00:01:02 +0000

This year, I only went for the Saturday afternoon session of FOSDEM 2009, the Free and Open Source software developers’ European Meeting. Two years ago, I mentioned the general trend that more women were interested in free/open source software/movement and this trend continues. But this time, I also noticed some really cute babies … and my son Neel-Alexandre was one of them of course! Although he’s only 7-month-old, he was really interested in the FreeBSD, Linux and Firefox mascots (respectively a red daemon, Tux the penguin and a fox). You are never too young to taste the truth ;-)

Baby movements during sleep

Tue, 27 Jan 2009 23:39:11 +0000

After a while, here is why I got a TV tuner for my Linux laptop, took screen captures and wrote a script to add a timestamp on pictures … I wanted to know how my (then 5-month-old) son was sleeping (his mom can be reassured: I was not planning to put electrodes on his scalp ;-) ).

Get the Flash Player to see this player.

var s1 = new SWFObject("../videos/player.swf",“ply”,“360”,“240”,“9”,"#FFFFFF"); s1.addParam(“allowfullscreen”,“false”); s1.addParam(“allowscriptaccess”,“sameDomain”); s1.addParam(“flashvars”,“file=../videos/081129-night.flv&image=../videos/081129-night.jpg”); s1.write(“container”);

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):

Pixel lapse under Linux

Sun, 21 Sep 2008 23:45:39 +0000

Finally, I got a working pixel lapse software under Linux :-) It’s a bit late (and I have to work tomorrow), code is rather dirty but I’ll publish it as soon as possible (btw that’s why I needed a webcam and a library to read it yesterday). Originally,

“pixel lapse” photography is the process of creating an image one pixel at a time. Beginning in the upper left corner, pixels are captured sequentially at a set rate until the entire image is formed.

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)

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):

Download YouTube videos

Sun, 02 Sep 2007 13:31:56 +0000

There are many websites around that allow you to download videos from YouTube. But it’s not possible to do it directly from YouTube. And you end up with a proprietary Flash video file. Although you can install the Flash plug-in on your computer, there are cases when you don’t want to do so or you are even not able to do so.

So, for whatever reason, you want a video from YouTube on your computer in a file format suitable for any kind of multimedia viewer? Here is a small (15 lines) bash script to download and convert a YouTube video you like in standard MPEG format. For that purpose, you’ll need wget (usually, you already have it on your GNU/Linux box) and ffmpeg.

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! :-)

Getting some TV news programmes

Thu, 19 Jul 2007 00:35:26 +0000

I told you it’s boring to lay down the whole day (see previous post). And even if I have a laptop, it’s very uncomfortable to type when you are on your bed with a leg on top of 3 pillows. Anyway, I’m not here to talk about my life but to share two small Python scripts. Their goal is to retrieve two television evening news programmes (from RTBF1 and France2, both in French). With that, I can directly watch evening news from my laptop (no need to browse their website nor install ad hoc Firefox plugin; everything can be done from the command line).

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).

Mapping cameras in Liege, 1 month later

Tue, 08 May 2007 00:34:37 +0000

Nearly a month after the initial launch of my map of CCTV cameras in Liege, quite a number of people contributed to add cameras on this map (some people contributed heavily ; thanks to all of them). Currently, we have identified 79 cameras but it seems we are far from finishing this work since, according to some sources, there were more than 109 CCTV cameras in Liege at the end of 2006! Did this put you at rest: 40 cameras added in one go?

How are you using tags?

Sun, 06 May 2007 00:37:26 +0000

I’m wondering how people are using tags and how it differs from keywords usage in the scientific literature.

Usually when I add tags on web services like del.icio.us or Flickr, I tend to add as many tags as possible. For example, even if a man is not the main subject of a photo, I’ll use the tag “man”. The rationale is we never know if, one day, I (or someone) would like to find a photo with a man and a tree (for example), the tree being the main subject. The problem is that I think I’m “diluting” the power of main tags. Another example … about a website helping find post-doc jobs, I’ll use the following tags: “jobs postdoc research science grants PhD job”. The problem is that “grants” is not really related (there are no list of available grants but only some jobs require grants and you never know what you’ll look for later).

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?

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 …

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:

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.

People love free e-mail services

Wed, 06 Dec 2006 01:47:10 +0000

… at least in my biased population. It came from a file containing all the people interested by ISAL and that I had to parse (the file, not the people). It’s a tab-delimited file with the names, e-mail addresses, location, interests, etc (in total, 379 unique e-mail IDs). I used Python for that purpose.

Since I had all the e-mail addresses in a Python set (*), I decided to do some stats. I know it’s useless but here are the results: 30.34% of Hotmail accounts, 27.18% of Yahoo ones, 7.39% of Gmail ones, 7.12% of Rediffmail ones (a popular e-mail service in India) and “only” 7.65% of KULeuven ones. As we can see, members mainly use free e-mail accounts (probably because the majority of them are students - the “S” in ISAL). And less than 10% of members come from the KULeuven, although ISAL is a students organisation from Leuven (the “L” in ISAL). Of course, R can produce nice charts. And since its documentation states that pie charts are “a very bad way of displaying information”, I also produced a regular bar plot.

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.

How to remove files ending with '~'

Wed, 15 Nov 2006 11:20:15 +0000

The vim text editor always produce a file ending with a tilde (~) as a kind of backup of the currently modified file (this is a default behaviour). On my MS-Windows machine (Pentium M, 1.73GHz), I was tired of manually deleting these files so I first used the “Search” option in the File Explorer. After some time, I got tired to wait for the results.

So I wrote a Python and a batch scripts to find all these files. They are going much faster than the Search GUI. The first time I launch them, they are still going slow (but faster than a GUI). As you can see in the graph below, the second time I launch these scripts, they went at least 10 times faster. I’m not a specialist but I guess it has something to do with caching at the OS level. For the first run, the batch script is 20% slower than the Python script. After that, the Python script is 50% slower than the batch script (but between 3.7s and 5.6s, the difference is not big).

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.

Dasher: where do you want to write today?

Wed, 18 Oct 2006 23:14:34 +0000

Hannah Wallash put their slides about Dasher on the web (quite the same as these ones from her mentor). Dasher is an “information-efficient text-entry interface”.

What made me interested in Dasher is her introduction about the way we communicate with computers and how they help us to communicate with them. There are keyboards (even reduced ones), gesture alphabets, text entry prediction, etc. I am interested in the ways people can enter text on a touch-screen, without physical keyboard. Usually, people use a virtual keyboard (like in kiosks for tourists or in handheld devices). But they are apparently not the best solutions.

Looking for a good free UML2 modelling editor ...

Wed, 04 Oct 2006 22:38:12 +0000

I was using Poseidon as a modelling editor for my UML2 diagrams. It was based on Java and I was able to run it from both GNU/Linux and MS-Windows. It was not free software but the Community Edition was free (as in “free beer”) and has all the tools I modestly needed. The only trick: all the diagrams had a string in the bottom, stating it was not meant to be used for commercial purpose (for educational purpose, I’ve written a small software that removes it).

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.

Stream redirection in Python

Wed, 06 Sep 2006 11:40:43 +0000

Two computers are on the same network. A firewall segregates the internet from the intranet. Both computers can access everything on the intranet but only one of them is allowed to access the internet. The problem is to listen to a music stream from the computer that cannot access the internet.

A possible solution is to run a stream redirection software on the computer that can access the internet. Then the computer that cannot access the internet can get the stream from the intranet (figure below).

Dissatisfied with blog systems

Sun, 23 Jul 2006 00:22:17 +0000

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:

Some thoughts about a family website

Sat, 22 Jul 2006 23:44:42 +0000

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

services will be based on existing free software (I don’t have time to develop a complete solution)
first service provided: a news service (I don’t know if it will be a forum or a shared blog)
second service provided: a photo gallery
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)
all this will allow everyone in the family to add elements, it will need very little maintenance and it should also be fast
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”.

Behavioural scorings reader

Sat, 03 Jun 2006 01:30:03 +0000

In our lab, we are (also) working on rodents behaviour. Some time ago, I wrote a very simple software that logs pre-defined behaviours to a file when the observer detects one of these particular behaviours and clicks on the ad hoc button. I accumulated quite some logs but I wasn’t able to really visualize how the rat performed. So, this evening, I wrote another small software to read those log files and to plot a graph of the rat activity. Here is a screenshot of the software in action:

Bioforum 2006, ISAL cultural evening, experiments ... A very busy week!

Sat, 20 May 2006 22:18:18 +0000

This week was quite busy … In the proteomic lab, I released the first version of IPGPhor2 Reader (see also the previous post). Of course, since we didn’t fail any recent experiment ;-) we don’t see the immediate usefullness of this software. The main purpose of this software is that it allows to see where and when an experiment failed, how the current was given during the IEF and when it was not correctly supplied.

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.

Using GD to draw a rainbow

Wed, 01 Mar 2006 22:17:42 +0000

I explain here how to use the GD library with C to draw a rainbow (or HSV scale).

Beginning with an IR camera

Mon, 30 Jan 2006 14:56:00 +0000

Two weeks ago, I bought a small IR camera on eBay. I received it this morning and I managed to have some time to test it. The camera is quite small (approximatively 15cm long, 10cm in height without the mounting kit) and comes from a Chinese factory ( Shenzhen Lianyida Science Co. Ltd ; I have the LYD-806C CCD model). The box is in plastic. It is said to be “weather proof” but, anyway, this one will stay indoor.

How to test the speed of an internet connection?

Tue, 03 Jan 2006 15:06:45 +0000

I was experiencing frequent disconnections of my internet link at home. These were very short but long enough to disturb one service I am using. So I decided to check if my internet provider was correct and doing his job correctly.

My first idea was that there must exists free (as in free speech) and simple command-line tools to test the connection speed under GNU/Linux. As I am not a specialist, I tried to find such tools on the internet but didn’t find any (if you have one, please feel free to share it with me). So I decided to write my own set of scripts in Perl.

Trying to use libpng

Tue, 13 Dec 2005 01:32:47 +0000

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).

Looking for a C++ widget toolkit for Linux

Thu, 17 Nov 2005 22:25:37 +0000

I am looking for a widget toolkit (a software bag of things that allow you to create GUI). I have two desideratas: I want to use C++ and I want to use it on GNU/Linux. I’ve found two big lists of widget toolkits: one on Wikipedia and one on atai.org. For the moment, I think of using gtkmm or wxWidgets but I need more information …

Now, some grumpy people will tell me they only use text-based applications ;-)