Month: October 2006

Search for images by sketching

On his blog, Laurent wanted to know who is this guy. I though it was an interesting starting point to see how good is Retrievr, “an experimental service which lets you search and explore in a selection of Flickr images by drawing a rough sketch”.

Although my drawing skills really needs to be improved (and their drawing tools more refined – always blame the others for your weaknesses 😉 ), a first sketch gives some interesting results (see screenshot below): 7 retrieved photos (44%) show a b/w human face in “frontal view” (if you count the dog, it’s even 8 correct images).

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If I just give the photo URL, results are not so good (see screenshot below). I am nearly 100% sure that it’s because it’s a greyscale photo scanned as a color image.

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When I upload the image on my harddisk, convert it to a greyscale image and upload it on Retrievr, now it gives more expected results: 10 images show a person with his/her hair (63%), either from the front or from the back.

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So this photo is not among the “most interesting” ones on Flickr (it is even probably not on Flickr). I suppose that if one applies Retrievr on a larger subset of photos, we’ll have a higher probability to find it (but it will also increase noise, i.e. the number similar photos). If you like playing with Flickr, other intersting Flickr mashups can be found here.

Automated Pubmed reference to BibTeX

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 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.

The problem with manual edition is that it is prone to error (even when copying/pasting from the web). Since Python programming is my hobby horse for the moment, there are two solutions to this problem:

  1. Use Biopython to get a reference from PubMed but are you ready to have a huge module dependency just to use 1 function?
  2. Write your own Python script, using a PubMed URL to download your reference and a little bit of XML parsing to extract the relevant info (one can use the ESearch and EFetch tools but my lazy nature tells me to simply use the URL).

Obviously, I chose to write my own Python script. Each reference from this PubMed XML format example (full DTDs) should be like this:

  author = {Poirrier, J.E. and Poirrier, L. and Leprince, P. and
Maquet, P.},
  title = {Gemvid, an open source, modular, automated activity
recording system for rats using digital video},
  year = 2006,
  journal = {Journal of circadian rhythms},
  volume = 4,
  pages = {10},
  pmid = 16934136,
  doi = {10.1186/1740-3391-4-10}

The script is here (4kb). First, use PubMed to check the reference you want, then take its PubMed ID (PMID) and launch the program, giving your BibTeX file in a pipe, for example:

./ 16934136 >> myrefs.bib

If you like, you can edit the script to change the tab size (here = 2).

How does it work?

  1. With PubMed, I do not use the correct tool but a HTTP query. It is much more simple and easier. The script asks for the PMID citations. Since it gets a HTTP answer, I need to parse this answer to replace entities (like , etc.) and obtain a valid XML file.
  2. Once I got the XML file and after some checking, I use XPaths from LXML (for me, XPaths are quick and dirty compared to write a DOM/SAX structure but it works!)
  3. Then the script simply prints the result to the standard output (even if it’s an error ; improvement : print on the error output). You simply need to get this output into your BibTeX file with the correct pipe.

Edit on October 23rd: this script has errors when dealing with non-ascii chars like “ö” in Angelika Görg. I won’t fix it for the moment.

Diwali 2006 @ ISAL

On Saturday, after the Kolam ritual, we went for Diwali, the Hindu Festival of Lights, organized by the ISAL. It was very nice to meet people we already met on previous ISAL “functions” and to talk with them. And I think that ISAL is attracting more and more people, both of Indian origin (working in Belgium, for example) and of non-Indian origin: this time, people from Belgium, China, Poland, Russia, Spain, etc. were there. As usual, I took some photos.

Kolam ritual @ Bozar

On Saturday, we went to see a Kolam ritual at Bozar. Kolam is the designs the Pulluvans are drawing on the floor for a lot of occasions, using multicoloured sands, rice and spices. Here, it was supposed to be a ritual for a family (“supposed” only because it was a demonstration for the public and no family was specifically involved). In this ritual, two women in a trance erase the drawings and answer questions the family is asking. The whole ceremony is linked to snakes that are supposed to have been in Kerala before men and that should be pleased in order to peacefully live together.

I took some photos but, unfortunately my camera isn’t good without flash (*). This ritual was part of the India Festival at Bozar. If you want some suggestions of things to see (dance, theatre, music, litterature, exhibitions, etc.), my father-in-law gave some here (in French).

(*) I found that people taking photos with flash during this religious ritual (even after the commentator specifically asked not doing so) are very coarse and insulting for the artists.

Symposium on Neuroproteomics in Gent

This friday, I attended the Symposium on Neuroproteomics organised at the University of Gent (B). Apart from Deborah Dumont‘s excellent talk, lectures were almost only focused on oxydative stress, neurological diseases and gel-free proteomics (like 2D-LC). One speaker even seemed to talk only to his computer or his presentation. So, it was not very interesting for me (finishing my thesis based on gel proteomics). The organisation was very “basic” and we even didn’t have any free pen + paper (fortunately, I took two pens and a notebook).

Dasher: where do you want to write today?

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.

They come with an interesting way of entering text, where pulling and pushing elements on screen are used to form words (with the help of the computer that is “guessing” the words from the previous letters). It requires a lot of visual attention but this can be turned into a feature for people unable to communicate with hands (for physical keyboard and mouse ; one man even wrote his entire B.Sc. thesis with Dasher and his eyes!).

You can download Dasher for a wide range of operating systems and even try it in your web browser (Java required) (btw, it’s the first software I see that adopted the GNU GPL 3). After reading the short explanation, you’ll be able to easily write your own words, phrases and texts.

They are interested in the way people are interacting with the computer. They are using a language model to show the next letters. On the human side, I am wondering if this kind of tool has an influence on how the human brain works. Visual memory should be involved in physical keyboard (“where are the letters?”) but also here (same question but the location of letters is changing all the time). Here, letters are moving but one can learn that boxes are bigger if the next letter probability is bigger. How is the brain involved in such system? What is it learning exactly? Are there fast and slow learners in this task? It could be interesting to look at this …

Proteom'Lux 2006

From the 11th to the 14th of October, I was at Proteom’Lux 2006, an international conference on proteomics held in Luxembourg. I presented a poster, learned quite a lot of information, met a lot of very interesting people and have now a clearer view on the directions and additional details needed in the proteomic part of my work. Some people presented some interesting new ideas (QconCat, MS-Blast, …). I am still assimilating all this information …

The conference schedule was very “tight” but, when I took some time to visit Luxembourg city a little bit, I found a place where I really wanted to enter 😉 Finally, it was also the first time I saw a biology lecture done in LaTeX Beamer (organizers also had a laptop with Ubuntu and an Impress presentation but it wasn’t apparently for a lecture).

Town and province elections in Belgium

Today, we were required to vote for the Belgian town and province elections (voting is mandatory in Belgium). A certain percentage of polling stations used an electronic voting technique. After identification, a person gives you a (presumably blank) magnetic card, you enter a voting booth, insert the card into a computer and, with a stylus, you point on a screen. The screen mimics a paper used in the old-fashioned way of voting: white circles on the left of a candidate’s name. After you voted, the computer gives your card back and you simply put it in a ballot box. If you want to know more about potential problems with electronic voting, you can look at Poureva, Recul démocratique and the Wikipedia article about electronic voting, e.g..

While looking for articles about electronic voting, I found this one about the perception of electronic voting in Belgium : “Electronic Voting in Belgium: A Legitimised Choice?” [1]. They tried to figure out:

  1. how easy/difficult it was for electors to vote on a computer: apparently, the vast majority of people find the procedure easy.
  2. to what extent they trust voting on a computer: apparently, a majority of people find this voting system trustworthy
  3. if they have a philosophical/social opposition to voting on a computer: apparently, nearly no one has an opposition to voting on a computer.

Although I don’t criticize their method, I don’t totally agree with their conclusion:

it seems quite clear that the introduction of electronic voting in Belgium is a choice that is legitimised by the vast majority of the population. More than 80 per cent answered positively to the questions regarding ease of use, confidence and social acceptance with regard to the new method of voting.

  • To legitimse is “to make legitimate”, “to make (something) legal or acceptable”.
  • Legitimate = “allowable according to law, or reasonable and acceptable”.

One has not to talk about the legality of electronic voting since, as they said, a Belgian law was passed to establish it. But we can ask on the way politicians passed this law. Do they asked citizens about it? Have they said that in their programme before election? The vast majority of the population can think that the electronic voting system is acceptable. But are they fully informed of all the ins and outs of such systems? If the governement absolutely needs an electronic way of voting, can’t it give the voters a way to verify the vote and observers a way to verify the votes after the election?

A simple way could be a small printer in the voting booth, printing the voter’s vote as soon as she/he takes back her/his card. This way, the voter can check if the machine correctly printed the vote. This vote is supposed to be the same in the magnetic card. And if one observer has any doubt about it (or anything else), one can still re-count votes with papers. The magnetic cards give a simple way to quickly obtain the results. The papers give a simple way to recount votes.

[1] P. Delwit, E. Kulahci and J.B. Pilet. “Electronic Voting in Belgium: A Legitimised Choice?” Politics, 25: 153-164 (copy).

Free communication at the BASS Autumn Meeting

I went to Gent, last Friday, to the BASS Autumn Meeting. With “New drugs for sleep” as a title and mainly physicians and psychatrists in the audience, I didn’t expected to have a lot of “basic science” presentations but the University of Liege was well represented by T. Dang-Vu, P. Peigneux, C. Schmidt and me in the free communications section (btw, we are all four from the Cyclotron Research Center). I outlined some recent findings on proteins differentially expressed after a short-term sleep deprivation. I had a nice question from Prof. Verbraecken (UZA) and, next time, I’ll focus more on pathways and physiological implications of proteins found rather than on functions only.