First tryout of Jadoo

Hi

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.

Oh yes, and I’ll try to add a decent CSS 🙂

Spice corner at Bozar Bazaar

Yesterday, we went for the Bazaar organised by the Bozar. While people were selling Indian bibelots and food (yummy!), Nandini set up a “Spice Corner” where she exposed and explained everything about Indian spices (you could even taste Pan Masala!). She had quite a success but, unfortunately for some visitors, Nandini did not sell anything. Our famous Peter also had a table for Rose vzw that was represented by Swapna (they were still there on Sunday).

Nandini and Swapna at the Spice Corner, Bozar Bazaar, December 9th 2006

The Bazaar was held in the Horta hall where we also were able to see performances by a folk Rajasthan group, a Bhangra group and two would-be Bollywood actors 😉 The theme was, obviously, Popular India.

Bhangra group performing at Bozar, December 9th 2006

In the evening we went to hear Asha Bhosle, the Queen of Bollywood songs. Although she has her age, listening to her real voice is a totally different experience than listening to a CD or watching a song from a film on DVD. I found this concert great!

From far, Asha Bhosle at Bozar, December 9th 2006

If you are interested in India, there are still some very nice evenings to spend in Bruxelles. Have a look at the Bozar website!

A nice 2D-DIGE difference

This week is very stressful because I am doing a 2200+ euros 2D-DIGE experiment (*) on samples from a rat organ we never studied before and from which I cannot obtain any more new samples.

We found a new pattern of proteins dispersion (compared to our previous experiments on other organs) and, more importantly, we found a clear difference in protein expression in at least 2 spots. In the image below, all the whitish spots mean proteins in these spots are found in equal amounts in the 3 conditions. But spots in red or green mean proteins expressed at different levels (even on/off) between conditions!

Difference in protein expression pattern in rat, revealed by 2D-DIGE

Now, we’ll have to perform a more mathematical/quantitative exploration of these expression patterns and hopefully identify these interesting proteins by mass spectrometry.

(*) 5nmol of Cy dyes (proteins labelling molecules) cost 2215 euros and weight something like 2.75*10-6g! I used nearly all that amount for my experiment. And I don’t take into account the 3-lasers scanner and common lab reagents

People love free e-mail services

… 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.

Pie chart of ISAL members e-mail accounts
bar plot of ISAL members e-mail accounts

With that very interesting information in mind, I’ll now be able to go to sleep (and work, because there is a lot of work that is waiting for me, this month!).

(*) a set is interesting because it could not contain duplicates and the file does contain duplicates.

Ruby France logo proposals

I couldn’t find sleep tonight (*) so I did two small variations on the Ruby official logo for Ruby France, since they are looking for a new logo (**). Double-clic to enlarge, single-clic to reduce back to the small images (***) :

 

I also like Greg’s proposal.

(*) it happens very often these days
(**) No, I don’t know Ruby
(***) Doesn’t work if javascript isn’t enabled in your browser (usually it is) + Internet Explorer doesn’t correctly render the transparency ; please use a real browser instead

Rose Annual Dinner

On Saturday, we went for the Rose Dinner 2006. Rose is an independent not-for-profit organization run by volunteers. Its mission is to support and foster primary education for children from economically disadvantaged rural communities in developing countries (mainly India), primarily by improving basic facilities in primary schools. Yesterday, its impressive team of cooks offered us great food (thanks Swapna), there was a good atmosphere. It’s good to see that people that actually do something in an effective manner. 🙂

We also met Peter (and his Dutch friend Peter) and, for once, we had some time to listen to his funny stories about some of his travels in India. And no, these stories don’t remove your will to travel to India (in fact, we are more eager to go back there). It was very nice to meet them.

And, finally, ISAL Christmas celebration will be held on December 16th (at 19.00), in Leuven. Save the date!

The Digital Ice Age

In this article, Brad Reagan gives many examples where the use of electronic data begins to cause problem, in a preservation perspective. The causes can be a new software that is not fully compatible with previous data models, new physical formats (unable to play old formats), too much raw information, etc. For the moment, free projects like the Internet Archive or the Free Archive (a.o.) are trying to cope with this problem.

Although the dangers of a “digital blackout” really exist, I think the author forgets one important aspect of information from the past: we already lost a lot of it. What is left is what time left us, often with some damages. It survived time, taking many different forms and paths, different storage procedures, different media, different locations, etc.

Instead of trying to store everything, maybe we should look at storing the most relevant information only. But now the question would be: how to know what is relevant and what is not? I vaguely feel that one can also add a notion of time: the e-mails I receive about a future party or a new product are not worth for more than 1 or 2 years although electronic exchanges that led to the discovery of siRNA, e.g., are much more important.

Plugins for Digital Object Identifier lookup

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.