Month: January 2006

Beginning with an IR camera

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.

photo of the IR camera

For this project (at work), we have an “outstanding” PC with an Intel Pentium II processor and running GNU/Linux RedHat 7. In this computer, we have an ATI Rage 128 with a TV tuner. We connected the IR camera to the computer, opened AVView (from the Gatos project) and we obtained a color image of things in front of the camera. For the screenshots below, I used a software written by my brother; pictures are in black and white because we are not interested in the colours (anyway, with IR LEDs on, images are B/W). With four white neons in a room without windows, we have this result:

B/W view with regular lightning
B/W view of my hand with regular lightning

When I switch off all the lights in the room, the IR LEDs from the camera are automatically switched on. The same objects with only IR LEDs:

B/W view with only IR LEDs
B/W view with only IR LEDs

We are monitoring changes in images. The problem is that all pixels are changing when switching from visible view to IR view. This change is not due to the experiment but is due to the observation system. I have to see how to cope with that in the results …

XML DTDs in biology

I was looking if a XML DTDs already exists for my field in biology (and, of course, I didn’t find any). It seems that is not available tonight (and wasn’t available before ; a WHOIS search told me that it is owned by someone from the bioperl project). I’ve found three collection of links to biologically-related DTDs: one by Paul Gordon, one by ( DTD repositories) and one by Andreas Matern. If you are interested, you can even try a seach in the registry. Most DTDs are focused on genes / genetics / genomics, proteins / proteomic, … but very few DTDs exist in other biological fields. And, of course, I am looking for a DTD in another field! All right, all right, I’ll try to write my own definition …

P.S. yes, this is another post full of links. It’s late and I’ll dig a little bit more tomorrow

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

Fosdem 2006 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// (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?

In fact, in Firefox as in many other browsers, the URL textbox is also a search textbox. In Firefox, when you enter something that’s not (exactly) an URL or if you enter words in the URL textbox, you are redirected to the Google “I’m feeling lucky” function.

Firefox search textboxes

This type of search does not gives you all the results (like a “normal” search) : it will redirect you directly to the first result. What happened to me was the following: I clicked on the wrong link, Firefox didn’t interpreted it as an URL and used the Google “‘Im feeling lucky” function. With Google, a search on “http” (the first word in the link) gives the Microsoft website as the first result. From Fosdem to Microsoft, this link is a bit surnatural 🙂

A lot of work

I have quite a lot of work. Therefore, I don’t have much time to post here. However, some days ago, I found this cool “ad” in another lab:

chemical products to sell?

The first time I saw this one, I thought one can buy alkaloids, fatty acids, etc. for 0.3 – 0.65 euros from there. But, I quickly understood that it was not the case: these are parts of notes you can buy. 😉

First presentation with LaTeX Beamer: RFT in fMRI

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.

Random Field Theory in fMRI

Slides in French and in English are available here.

A special Belgian e-ID for foreigners? Bad Idea!

This last week-end, a Dutch-written Belgian newspaper wrote that the Minister of the Interior, Patrick Dewael, is planning a special electronic ID card for foreigners in Belgium. If this become reality, every foreigner in Belgium will have an e-ID with his/her biometric data inside, even if he/she is officially living in Belgium, with a regular permit to live, work, etc. Of course, this project is aimed at illegal foreigners (btw, have a look at his other “brilliant” idea: heavily punish those who are helping illegal foreigners to obtain asylum, regular papers, etc.). Thus it seems there will be two versions of this card. Their official reason is “better control”.

I first think it’s a very bad idea because no one will be equal in front of the law, police forces, etc. You can keep you “special foreigner e-ID” in your pocket but once you show it to someone (to identify yourself in a bank, in a car rental office, …), it will be humiliating. And there is a risk that some people will refuse to interact with you because of this card.

This e-ID is only a tool, I agree. But it will be created with a bad intention in mind. In a previous post, I didn’t dare to say that the “regular” e-ID was created in order to control Belgians. This “foreigner e-ID” is created expressly to control foreigners in Belgium. The technical questions about who will be able to read information on the regular e-ID and how it will be done, within which legal frame ; these questions are not yet solved. Now that it’s technically possible, nauseous ideas are appearing …

If you know French, you can read some reactions in La Libre Belgique (there is a video but I cannot see it (obscure MS format unreadable with free software)).

A step further "simple" Open Access to scientific litterature

Combining a trend from the free software world and a reaction to increasing subscription costs, the last decade saw the emergence of the “Open Access” movement in the scientific litterature. Instead of transfering all your rights (and copyrights) to an editor that will sell your work to other scientists, you can choose to publish your work in Open Access journals. In this case, you retain your rights (and copyrights) on the article you wrote. Moreover, your work is freely available to other scientists (at least in electronic format) while still being of some quality since the reviewing process is still there. As an article writer, you only risk to be cited more often (since your article is freely available). As an article reader, you only risk to gain more knowledge (since more and more interesting articles are published with various Open Access publishers like BioMed Central, the Public Library of Science, etc.).

Now, I recently discovered Science Commons, a kind of extension of Creative Commons for sciences. Most Open Acces publishers chose one of the Creative Commons licences for the articles and additional material they offer. I’ve not yet read everything on their website. But this initiative seems to be a nice “enhancement” of giving access to the scientific litterature since they go a step further by focusing also on material licensing and the accessibility to raw data.

Of course, one of their projects deals with publishing scientific litterature. For me, this project can bring a bit more “independent” discussion in the field (by “indenpendent”, I mean that they don’t seem related to any publisher although they promote Open Access, of course). What’s more interesting is their two other projects because they can bring some fresh air and new ideas in their respective fields.

Science Commons second project deals with licencing material (hardware). It will explore standard licensing models to facilitate wider access to scientific materials. Without material, we cannot do science (it’s not Philosophy, working on ideas, concepts, etc.). Sometimes, material is so specific that it’s not sold by any big pharmacological / biotech companies but only produced on demand by another lab, in another corner of the earth. For the moment, nearly every material transfer between two labs is associated with a specific transfer agreement. Some standardisation will allow scientists to focus on their work rather than on legal and administrative annoyances while still giving rights and credits to the right group / people.

Finally, the third Science Commons project explores ways to assure broad access to scientific data. If you are lucky to publish your findings, maybe someone will find other effects or give you hints to find other relevant facts by simply looking at your raw data. This will allow a quickly evolving science and, for example, it will avoid the unneccessary use of many more laboratory animals, just to reproduce an experiment and trying to find other or more effects than those already published. Now if your experiments did not worked, for any reasons, publishing those unsuccessfull results will also prevent other people from performing the same unnecessary experiments. In biological sciences, it’s often difficult to publish a paper on, e.g., the fact that iron has no effect on a some metabolism. But I think it’s worth publishing data from this experiment since it can give clues on other substance effects on some biochemical pathways.

I know this post is rather biological sciences oriented (I am sorry, it’s my field ; and I didn’t even wrote about the NeuroCommons project, part the Science Commons Data project). I suggest you to have a look at the Sciences Commons website and to see by yourself how it can help your science field.

And I thought I had stress before my presentations …

There is a story on how Steve Jobs prepares his talks for Apple’s keynotes in the Guardian Unlimited. Well, it doesn’t say much about the preparation in itself. But I can feel the stress Mike Evangelist is experiencing: he had to talk in front of hundreds of people, in front of his boss and present software not yet finished. And I thought I had stress before my presentations …

Of course, there is another reading of this article. OK, Apple is a small technology company. But it developped a good sense of communication. When you are buying an ipod, your are not only buying a portable music player (btw including imprisoning DRM): you are also buying a feeling (of hype, of having the last gadget, …). When you are buying a Mac computer, it’s also a feeling of being part of “another” community, … Apple cultivated this feeling since the beginning with slogans like “Think Different”. And, of course, this article, the book Mr Evangelist is trying to write, … even this post on this blog, they all participate in the “buzz” around Apple keynotes. Finally, if this noise (*) wasn’t there, Apple will only be another computer-selling company.

(*) in signal processing, noise is what intefere with the signal. Only the signal (Apple products) might be important. Noise is there to disturb, enhance, distord, … the signal.

How to test the speed of an internet connection?

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.

For the moment, results are somewhat convincing (but the “ping” command does not reflect exactly the connection speed) but they can already be used 🙂

Example of results (image is reduced)

You can find scripts, how to do it and work in progress here.