This evening, I prepared a computer for the lab. Don’t blame me but it has to be under MS-Windows and with MS-Office. Knowing it’s only an Intel Pentium II MMX (“x86 Family 5 Model 4 Stepping 3”) with 64Mb of RAM and 2.4Gb of hard disk, I needed to find general software that has the smallest footprint in terms of both memory and hard disk consumption. Here is a small list of software I found interesting (mainly for me to remember): ...
Finally, a second scientific paper is published by the Poirrier-Falisse (a first paper for me): Poirrier JE., Poirrier L., Leprince P., Maquet P. " Gemvid, an open source, modular, automated activity recording system for rats using digital video". Journal of Circadian Rhythms 2006, 4:10 ( full text, doi) It is still in a provisional PDF version but already available on the web and Open Access (of course)! Here is my BibTex entry. I will upload source code tonight on the project website.
Today, I did some “spot picking”. In 2D electrophoresis, you disperse proteins in a gel according to their electric charge and mass. You obtain a kind of map of proteins and, if you stain these proteins, you have a map of spots ( example here). After some analysis, it could be good to identify some proteins of interest. The problem is that they are in the gel! So, today, I used a robot called “spot picker” that … picks spots representing proteins of interest out of the gel. You can see what a spot picker looks like in my proteomic set on Flickr.
Nandini published her first paper in a scientific journal: Falisse-Poirrier N., Ruelle V., Elmoualij B., Zorzi D., Pierard O., Heinen E., De Pauw E., Zorzi W. Advances in immunoproteomics for serological characterization of microbial antigens. J Microbiol Methods. 2006 Jul 3 ( DOI access). Congratulations! :-) It is still in electronic format (ahead of print) but already available on the web (but not Open Access, unfortunately ; I think Nandini will auto-archive it somewhere). Here is Nandini’s BibTex entry (will be updated for volume and pages asap).
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 ...
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.
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: ...
This morning, the temperature in the animal housing unit was 10.5°C in all the rooms and 13.7°C in the room where the rats are sleeping. As explained in the ad hoc page of the university website, they turned the general heating system off since May, 15th, regardless of the weather conditions. Since then, I’ve clearly observed a drop in temperature. But today is the worst, not only for scientists who are trying to work in these conditions but also for the precious animals we take care of (the recommended temperature range by all ethical committees is 20-25°C). ...
This week was quite busy … In the proteomic lab, I released the first version of IPGPhor2 Reader (see also the previous post). Of course, since we didn’t fail any recent experiment ;-) we don’t see the immediate usefullness of this software. The main purpose of this software is that it allows to see where and when an experiment failed, how the current was given during the IEF and when it was not correctly supplied. ...