Like computer hackers who cooperate in developing and using tools to understand and manipulate the inner workings of computer software, researchers are developing sophisticated biological methods that will allow them to crack the function of the genome. Daniel Evanko shortly writes about two methods to probe the function of the genome: cDNA sequencing and microarray hybridization. It’s in Nature Methods 3, 495 (2006): abstract - full text (a post just to show that biologists are also hacking their stuff)

In his blog, Jonas Hielscher wrote about an animal controlled computer game), where a player can play Pacman against real crickets! It is so cool, I shamelessly copy and paste his screenshot here : I find it cool to see nice application of tracking, like I did (tracking) with my rodents: Tracking of a rat in the Morris water maze rat = big, red spot on top its trail from bottom is also in red ...

In the June/July 2006 issue of Scientific Computing World, there is an interesting article about Andre Geim, director of the Manchester Centre for Mesoscience and Nanotechnology. Do you remember the levitating frog? It’s him (he even got an Ig Nobel prize for it). Do you remember the “gecko tape” ? It’s also his actual group! So, in this article, they wrote about Prof. Andre Geim story, from his early school days near the Black Sea and in Moscow to the various labs he visited and worked with in the past few years. Although he works in nanotechnology, some of his quotes can easily be applied to biological sciences (where I am not doing “mainstream” experiments like stem cells, genomics, fMRI, etc.) … ...

Especially when one loses a beloved aunt …

This Friday (June 23rd), we went to IMEC, a research center in nanoelectronics and nanotechnology (in Leuven). We weren’t there for the technology but because they organised an afternoon with Indian dances, songs, etc. We were only able to attend the last few dances but we met people from ISAL (I am tempted to add: “as usual”). It was nicely done with posters explaining some Indian traditions, huge flat screens showing Bollywood dances and food (of course). Looking for more informations on their website, I see that they have a bioelectronics section where they are studying neurons interactions with electronic chips :-) (a.o.). Unfortunately, there isn’t any jobs for biologists in this department for the moment.

Last Friday, I was still in my wife’s lab at 19.45. It’s on the 4th floor of the Liege Hospital. From there, I could see the parking lots (for visitors). Far away, the free parking lots were congested, as usual. But I was more interested in the paying parking lots, the ones that are the nearest from the hospital. Despite the fact that it was 19.45, there were still some cars. Some cars were there since the morning or the afternoon but some of them were just parked there a few minutes ago. I tried to draw where the cars were. ...

… at least if you are a biologist interested in genes, genomes and pathways. KEGG is the acronym for “Kyoto Encyclopedia of Genes and Genomes”. I’ve found it while looking for genes involved in the circadian rhythm and in the long-term potentiation and depression. Of course, for a biologist strongly interested in computerised treatment of biological data, it’s a bit disappointing that these pathways in the KEGG PATHWAY Database are manually drawn but, well, it remains a very usefull tool to continue and digg further in the comprehension of these mechanisms.

This week-end, I attended a scientific meeting and, although the content of the presentations were often interesting, they also often lacked attractiveness. This reminded me two videos I stored, some time ago, on my hard disk. Sébastien Lorion called them “refreshing”. And, for me, not only these presentations look beautiful, they also talk about an interesting topic: who are you on the internet ? In the first presentation (a keynote at OSCON 2005), Dick Hardt talk about what is identity and how do we prove who we are, in the online world. ...

Sunday, we went to a restaurant with my in-laws. They used to go there since a long time and they personally know the restaurant owner. Each time they eat there, it’s an opportunity to chat about the respective families ; so, when my wife is with her parents, the owner remembers what my wife is doing in life. But, since a few months, we went there three or four times alone (i.e. just my wife and me) and the owner never recognised my wife. ...

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: ...