Lab-Life

I don’t consider having more or better ideas than others. But I gradually realized I have less and less time for some activities like programming, electronics etc. Maybe that’s how we realize we are getting older now adults. So I decided to share these ideas rather than fueling the illusory idea that I will implement them one day. So idea 1 is about measuring sleep. I recorded animals’sleep during my Ph.D. - but it was thanks to an EEG device. I think that if you want to understand or improve something you have to first measure it in a way or another. So I started to try to measure my own sleep with an app ( Sleep Cycle). But despite its good reviews it doesn’t work, at least for me. ...

The US FDA recently approved Proteus Digital Health Ingestion Event Marker ( IEM). Basically, it’s a pill with some electronics attached (very tiny electronics: around 0.5mm in diameter for a total weigth of 5mg, see picture below). Once activated the pill transmit a signal and, coupled with a detector, you know when the pill got into your body. Edible sensor for electronically confirming adherence to oral medications. ...

This afternoon I received a bunch of data accompanied by stacked bar graphs for each dataset. For example, this one: The chart shows the incidence of disease X in various age ranges. That incidence is split by 8 severity levels. The chart shows that the disease especially affects age ranges 4 and 5, at different severity levels. However I didn’t feel comfortable … what are the different levels of severity in age ranges 1, 2 and 3? how can we compare levels C, D and E in age ranges 4 and 5? is there anywhere some severity A? (it’s even worst when some age ranges don’t have any incidence at all: what is happening?) etc. I looked on the web but couldn’t find much information apart from the fact " The Economist says they’re so bad at conveying information, that they’re a great way to hide a bad number amongst good ones" (but are still using them in their graphic detail section) or " a stacked column chart with percentages should always extend to 100%" (this doesn’t really apply here). Then in a post on Junk Charts, someone mentioned Steven Few who would have said “not to use stacked bar charts because you cannot compare individual values very easily and as a rule [he] avoid[s] stacked bars with more than six or seven divisions”. And Steven Few also participated in his forum here. ...

Reference Manager is a commercial reference management software package. It is extensively used in biomedical research, along with Endnote (sold by the same company), mainly because the main OS in these labs is Windows from Microsoft. I used it at the university and still have some reference databases in its format (with file extension .rmd). This evening, I had to go back into one of those proprietary, closed databases I still had (most of my references were later re-entered in a BibTeX file). I could have borrowed my wife’s computer running Windows or tried some Open Source software that can open .rmd files. But it would have been too easy. So I tried it with Wine, a program that allows Microsoft Windows applications to run under Linux. In Wine AppDB, it is written people had tried version 9 and 11. In the old time, I bought a student license for version 10. ...

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. ...

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). ...

FluTE is an influenza epidemic simulation model written by Dennis L. Chao at CSQUID. It works out-of-the box on GNU/Linux (just type make and run it). I wanted to see how it works. But since I’m temporarily stuck with a Windows laptop, I downloaded a free C++ compiler for Windows ( wxDev-C++), imported all the files in a project and compiled. For those who want to try, here is the project file and the specific makefile in a zip file (2 kb). Just decompress the FluTE archive (I used version 1.15), copy the two files from the zip file above and launch the IDE. In the project options (Alt+P), specify the custom makefile (in the “Makefile” tab) as the one from the zip file above. Compile (Ctrl+F9). Done. ...

As I promised before, you’ll find here the text and slides of my Ph.D. thesis (btw text and slides are in French). The oral presentation was on March 24th, 2010 and everything was fine :-) Slides can be watched below. Effets du sommeil et de la privation de sommeil sur le protéome hippocampique de rat après apprentissage topographique http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=3557617&stripped_title=effets-du-sommeil-et-de-la-privation-de-sommeil-sur-le-protome-hippocampique-de-rat-aprs-apprentissage-topographique-3557617 ...

It’s the impact factor of the Open Access journal Proteome Science where I published my last article, last year. I didn’t see that before but came to know when I downloaded the 453 remaining e-mails from an old account (3 months without fetching them). The announcement of this new impact factor was in one of the three interesting e-mails.

I often wrote about Pubmed here. Briefly, it’s a search engine for publications in the biomedical domain. They recently redesigned their user interface and, although there are a lot of new things to save time that came with the new design, there is still a problem with their interface: the new search box takes too much space … Redesigned Pubmed homepage ( bigger image) Redesigned Pubmed result page: search box is hiding the logo, the display settings and the first result ( bigger image) ...