Category: My life

A good issue of Nature, obviously!

The October 14th, 2010 issue of Nature is obviously a good one. It had to be a good one! I usually advocate Open Access but it is always nice to reading complimentary issues of Nature which is Closed Access but is also publishing very good articles about science at the same time.

In this issue, I was interested in various topics …

First, there is a serie of articles about the US midterm elections and what (US) scientists feel about two years of Obama administration. Obama promised total transparency in American science, a new era of integrity and more freedom for scientists. From what I read, this isn’t the case yet.

Then, there are two article about publishing computer code from scientific experiment. In a World View, Nick Barnes, director of the Climate Code Foundation takes some concerns about that to pieces. The main reasons to provide computer code is to improve programming skills (the software author’s and others’) and enable others to engage with your research. Don’t be ashamed of the quality of your code. Don’t be afraid of starting the trend if no one around you share their software. Don’t be afraid to refuse support when badly asked for. Don’t overestimate the intellectual property value of your code. Nick Barnes also wrote a blog post about it. And you can comment on the Nature article here.

In a News Feature, Zeeya Merali tells stories of scientists who found themselves in uneasy positions regarding to the software they wrote but, at the same time or later on, realised publishing their software was the best thing to do. Besides formalising one’s training in programming, Zeeya Merali advocates some simple steps to practise “safe software”: use a version-control system ; track sources, data and events ; write testable software ; test the software and encourage sharing of software.

I was also interested in these articles in two ways. First, I also realised the need of a formal training in programming during my Ph.D. and I eventually got a B.Sc. in computer science. In the team and field where I’m now working (Health Economics and modelling of infectious disease), I can clearly see the benefit of having such training. Don’t get me wrong: I meet wonderful colleagues every day who don’t have the training but have lots of skills and can solve lots of problems ; I just often see the ease to grasp algorithms as well as some better procedures and testing that comes with training. And, second, I would like to addd that free software licences are to be considered when publishing your software (for science or not).

In the same issue, there was also a small news about the Europe’s use of research animal. This reminded me of the good-old-days :-). Fundamental biology still account the largest proportion of animal experiments but what intrigued me is the 12.2% of “Other” usage.

There was also a comment on a book, The Professional Guinea Pig, about paid participants in phase I clinical trials. Interesting perspective from “the other side” of trials.

There is also an Outlook on the Lindau Nobel Laureate Meeting. It features interviews with 10 Nobel laureates (it’s always nice to readd their comments on science) and an article about science in the digital age (not yet read but it seems interesting).

Finally, an ad for my previous lab (GIGA ULg) caught my attention, as well as the small article about Science in Belgium. I must however write that this article is a bad summary of the research landscape in Belgium with, for example, mention of only two universities: the KUL and the UCL (we have many more). Souvenirs, souvenirs.

Happy Software Freedom Day 2010!

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).

In terms of user experience, you can’t beat the installation process of Ubuntu (my comparison criteria are Fedora 13 and any version of Windows XP, Vista or 7 that are not on a PC-specific image disc). Seven configuration screen with rather simple questions and that’s it. There are choices you can’t make like the selection of software you want to be installed and available on the next reboot. But, most of the general software is there: a web browser, a word processor, some games, a rudimentary movie player and a music player. The “Software Center” is also readily visible so you can’t miss it and it seems to be an obvious choice if you want to install any other software.

New Ubuntu desktop for Freedom Software Day 2010

The real test will now be if one can actually work with it. If I don’t post any furious comment against some features or if I don’t post anything about the installation of some software in the coming days / weeks, you’ll know I’m still working with this Linux flavour.

Les bien étranges manières de Test-Achats

(Post in French regarding the strange manners of a French-speaking Belgian consumer association: Test-Achats)

Test-Achats est une association de défense des consommateurs belges ainsi que le nom de leur magazine mensuel. Je veux lire un de leurs articles sur leur site web. C’est impossible, il faut s’abonner. Payer pour lire un article me paraît normal (une personne a travaillé pour écrire cet article). Mais il aurait été intéressant de pouvoir acheter l’article à l’unité plutôt que de devoir s’abonner pour pouvoir avoir un code d’accès aux archives et seulement lire 1 article (vente liée ?). Passons.

Avant de remplir le formulaire d’abonnement, je me dis que cette association commence déjà bien comme les sites de vente par correspondance (avec toutes les connotations négatives que cela suppose) où le client est attiré par :

  • un offre “irrésistible” avec période d’essai de 2 mois
  • un gadget très utile (une chaine “hi-fi”)
  • un deuxième gadget très utile (un appareil de mesure des distances)

La dernière fois qu’on a eu un abonnement à Test-Achats, chez nous, j’étais toujours chez mes parents et les gadgets n’ont fonctionné qu’une semaine … sans parler du super PDA avec appareil photo … photo de peut-être 45 pixels sur 20 sur un ensemble de pixels de même résolution faisant office d’écran noir et blanc quand les Palm les moins chers faisaient mieux pour peut-être 100 euros. Mais il est vrai qu’ils sont gratuits : on ne peut pas s’attendre à des miracles non plus !

Je commence donc à remplir le formulaire d’abonnement quand même. Sur la première page, une case à cocher m’indique que si je ne souhaite pas que Test-Achats utilise mes données pour me faire découvrir ses autres produits, je n’ai qu’à cocher cette case. Cà s’appelle du opt-out.

Test-achats : faux opt-out

Comme je ne souhaite pas vraiment découvrir les autres produits (livres, etc.), je coche. Et là, un message d’erreur me dit que sans mes données, il est impossible d’envoyer les revues. Euh … non … je veux bien les revues (l’abonnement) mais pas les publicités pour les autres produits. Soit ils ont codé leur base de données et leur site web avec les pieds, soit cette “erreur” est délibérée pour obliger les clients à la cocher. A quoi sert cette case, à part à donner “bonne conscience” à Test-Achats ? A rien.

Test-achats : erreur trompeuse pour opt-out

Je coche la case pour pouvoir continuer : ce ne sera pas les seuls papiers non solicités que je reçois dans ma boîte aux lettres (malgré l’autocollant refusant la publicité / “presse” gratuite) …

A l’écran suivant, on arrive à l’écran de paiement. Encore une case à cocher inutile : j’autorise ou pas le prélèvement sur mon compte, à l’issue de la période d’essai. Non, je n’autorise pas : vous n’avez qu’à m’envoyer un formulaire de paiement (ou même de domiciliation) par la poste ou e-mail à l’issue des 2 mois. Ah, c’est encore une fois impossible : décocher la case provoque aussi une erreur. L’erreur dit que l’autorisation est obligatoire pour completer la commande.

Test-achats : impossible de ne pas payer par domiciliation

Il y a bien un autre moyen de payer : par carte de crédit. Et là, ils ont au-moins la décence de ne pas mettre de fausse case à cocher : il faut payer. En fait, je suppose que la case à cocher pour le virement automatique sert de “signature” alors qu’il n’y en a pas besoin pour le paiement par carte de crédit : le processus de paiement par carte inclut déjà un processus de signature électronique.

En résumé :

  • obligation de s’abonner pour pouvoir lire 1 article
  • une offre “irrésistible” et 2 gadgets inutiles
  • un faux opt-out pour les autres produits
  • une fausse case à cocher pour autoriser le prélèvement automatique

Finalement, je remarque que la mention de la durée de la période d’essai (2 mois) n’est plus présente depuis le début de la procédure d’inscription. Serait-ce pour ne pas que le client s’en rappelle et, comme je suppose beaucoup de gens, laisse passer la période d’essai et se retrouve abonné, plus par “paresse” que par réelle volonté. Dans d’autres périodiques, la période d’essai ne nécessite pas de coordonnées bancaires, réclamées seulement à la fin de la période (avec insistance parfois) ; et si elles ne sont pas fournies, l’abonnement est tout simplement arrêté.

Je ne terminerai donc pas de rempir ce formulaire. Je ne lirai pas l’article qui m’intéressait. Mais je ne serai pas non plus abonné à une revue de force et je ne recevrai pas de spam dans ma boîte aux lettres.

Let my dataset change your mindset

In the previous post, I shared a video of David McCandless giving a talk about information visualisation. One phrase caught my attention and a bit of research lead to a very good discovery. The phrase and context is (emphasis is mine):

We need relative figures that are connected to other data so that we can see a fuller picture, and then that can lead to us changing our perspective. As Hans Rosling, the master, my master, said, “Let the dataset change your mindset“. And if it can do that, maybe it can also change your behavior.

Who is Hans Rosling? A Professor of International Health at Karolinska Institute and Director of the Gapminder Foundation (from Wikipedia). Nothing fancy nor anything related to information visualisation at first sight. Except that the Gapminder Foundation is “a non-profit venture promoting sustainable global development and achievement of the United Nations Millennium Development Goals“. So what? Gapminder also “pursue[s] the development of the Trendalyzer […] [seeking] to unveil the beauty of statistical time series by converting boring numbers into enjoyable, animated and interactive graphics“.

And this software is really great (see screenshot below but, above all, in all Rosling’s videos): from one single interface, you can gather lots of different types and sources of data (about the development of the countries of the world) on the same chart and it nicely display them along more than the two dimensions of your screen. Bubble sizes and colours represent other dimensions. And the whole thing move with time (years).

Trendanalyzer screenshot

What is also very interesting is that you can play with Trendanalyzer (in Gapminder world) and download the data behind it. In addition, Google acquired Trendanalyzer and offers some of its components as a “gadget”: Motion Chart.

The beauty of the software is nothing without appropriate use. And in all of his videos, Hans Rosling makes appropriate use of data visualisation, succeeding in converting messages heavily relying on statistics and various sources of data (not something usually visual attractive) in simple visualisations. As David McCandless said: “It’s effortless; it literally pours in”. By visualising it in such a way, it’s more easy for the dataset to try to change your mindset.

Because the tool isn’t everything. With its help, Hans Rosling is trying to convey messages. And if you watch any of his videos, you’ll see that he effectively succeeds in doing it wether it’s to make you stop talking about “developing” countries or to make you think about the role of the end of poverty in the growth of world population, for example. In his Six Minutes blog, Andrew Dlugan summarises Hans Rosling’s technique in 6 points:

  1. Explain the data axes
  2. Highlight subsets of data
  3. Dig deeper to unwrap data
  4. Place labels close to data points
  5. Answer the “Why?” questions
  6. Complement data with energetic delivery

Hans Rosling presenting The seemingly impossible is possible at TED 2007

Althought some of these techniques were taught or discovered by own practise during B.Sc./M.Sc./Ph.D., the combination of them make a presentation very effective, even in front of a small audience.

Why do I blog this? I watched all Rosling’s videos in one go. Once the current presentation was over, it was difficult to resist to watch the next one. From a general perspective, I’m very interested in all means to ease the way people can grasp huge amount of data and to maintain their interest during presentations. From a more practical perspective, I’m starting to deal with some amount of information for various projects and I’m looking for attractive ways to show them. And I was about to forget Hans Rosling is professor of Global Health, a field close to my current one: Health Economics. You couldn’t dream of a better thing than learning more about your field with interesting ideas and appealing presentations.
What triggered the redaction of this blog post is the release of a 55-minute documentary about Hans Rosling’s life and thoughts on YouTube.

David McCandless on information visualisation

Tonight, I realised that David McCandless was behind informationisbeautiful.net, a blog dedicated to information visualisation which I often mentionned before on this blog.

David McCandless speaking at TED, July 2010

Last month, David McCandless gave a talk at TED, a NGO “devoted to Ideas Worth Spreading”. And it was very interesting to hear him, to put a living face on a blog and to apprehend the amount of work to make such great infographics simple to understand. Here is the video (thanks to the license: CC-by-nc-ndon this page, there is a link to download the high quality video):

http://video.ted.com/assets/player/swf/EmbedPlayer.swf

Why do I blog this? I was always and I am still interested in information visualisation, could it be from others (like the flu tracker or, more modestly, my own attempts (to stay in the flu topic). As David said, everyday, everyone of us is blasted by information design, it’s being poured into our eyes, it’s a “dormant litteracy”. And I am curious of new ways of visually presenting large datasets like at the Hack.lu 2009 InfoVis Contest or results of time-consuming models of disease spread.
But of course, on the other hand, you have to ask the right questions, look from the right angle: the one who master information design may also influence the minds of those who see this information and, more importantly, its interpretation. David McCandless didn’t say anything about this: the responsability of the designer regarding the interpretation of his/her design.

"Facts & data"

A colleague of mine is always hammering home the message of bringing facts and data to a discussion rather than rumors, hearsays and daily newspaper articles. Since a few days (because H1N1 is not a pandemic anymore?), newspapers are coming with another “Superbug” or “Germinator“, wrongly named “NDM-1“. So, before spreading fear, uncertainty and doubt, please read the scientific litterature or, at least, read quality newspapers (articles from The Guardian are quite fair and balanced).

NDM-1 (New Delhi metallo-beta-lactamase) is just the name of a gene in a plasmid that two bacteria at least, K. pneumoniae and E. coli, can carry. This gene makes bacteria resistant to almost all antibiotics. If you want to know more about this gene, Yong’s paper characterised it (access without subscription). Health care agencies know about this issue at least since last year.

Now, you can still go to India and Pakistan. New Delhi is still a safe city to visit. But yes, in general, the world will face a problem in the future because bacteria are becoming resistant to more and more antibiotics.

Summer in Scotland

We are back from Scotland and it was really amazing. “Awesome!” (as they would say in another part of the world). You can’t imagine how beautiful is the landscape, how rich is the biodiversity (although we were in the West, where they said “God had no earth left when he created Scottish Highlands”) and how kind are people.

We spent lovely nights at the Rowantree Cottage in Arrochar. It was the first time Neel called someone “The Gentleman” (Bill Thompson) and “The Lady” (Irene Thompson), our lovely hosts. And Charlie the cat was also very kind and patient with Neel.

In Rowantree Cottage
In Rowantree Cottage

If you have time, we definitely also recommend The Ballyhennan restaurant, situated between Arrochar and Tarbet. In a beautifully renovated 18th Century former church (*), the service is very warm and the food excellent. Try it with or without your family, its food is really excellent and will please everyone!

(*) we learned and saw it’s very common in Scotland to transform lovely churches into restaurant, bed and breakfast or private houses.

In West Scotland, you can’t miss Loch (lakes) and mountains (and midges too, when it just rained and the sun appears). Driving there is very funny (especially on B type roads!). And everywhere you go, you want to stop and just look at the beautiful scenery around you.

Fun at the lake
Fun at the lake

In Ardnamurchan, we also spent lovely moments at Craig Na Shee, the Rock of Peace. When you arrive there, you wonder how they managed to fit all this comfort in a remote place. And then you sit, relax and enjoy the place! (We were so relaxed we even forgot to take a picture of the great house.) If you have the chance to have good weather conditions (i.e. not too much rain) – and we did, one day – go and visit Sanna Bay, a wonderful bay on the Atlantic ocean.

Sanna beach
Sanna beach

So you have to discover Scotland, it’s wonderful!

Scotland valley

Thank you for the bread

First evening after first day of work after holidays, we decided to keep the dinner simple: rice and sandwiches (“bread” for The Little One).

As usual, he couldn’t easily find sleep (but finds every possible excuses not to sleep). When it’s my turn to go and comfort him, he finally decides he’ll go to sleep with Bow-bow, his plush dog …

Dad – Good night, Neel
Son – Good night, papa
Son – Thank you for the bread

Then how not to melt? I love you, Son.

Tetris wall

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:

Tetris wall 1

Tetris wall 2

Jean-Etienne 😉

Photos found on Olybop.info (without original credit). Other walls with Tetris can be found on Flickr.

Cognitive Surplus visualised

In the 300-and-more RSS items in my aggregator this week, there are 2 great ones from Information is Beautiful, a blog gathering (and publishing its own) nice ways to visualise data.

The first one is based on a talk by Clay Shirky who, in turn, was referencing his book Cognitive Surplus. In Cognitive Surplus visualized, David McCandless just represented one of Shirky’s ideas: 200 billion hours are spent each year by US adults just watching TV whereas only 100 million hours were necessary to create Wikipedia (I guess the platform + the content) …

Cognitive Surplus visualised from Information Is Beautiful

It makes you think about either the waste television helps to produce either the potential of human brain(s) if relieved from the burden of television.

The second interesting post appeared in fact in information aesthetics, a blog where form follows data (referencing Information is Beautiful but I can’t find this post). In Top Secret America: Visualizing the National Security Buildup in the U.S., Andrew Vande Moere relates “an extensive investigative project of the Washington Post that describes the huge national security buildup in the United States after the September 11 attacks”. The project website contains all the ingredients for a well-documented investigation with the addition of interactive maps and flash-based interfaces allowing the user to build his/her own view on the project.

Top Secret America from the Washington Post

It’s nice to see investigative journalism combined with beautiful data visualisation and handling!