Month: March 2007

Unlimited storage in online apps

Although I liked Bill Burnham’s post about the “storage explosion” I think he forgot one thing in one of his last posts. In “YahooMail, Storage, and the Battle For Personal Data” he explains the announcement of unlimited e-mail storage for free by Yahoo! is the indication of two trends: for him, the obvious one is that storage is cheap and the less-obvious trend is that there will be a battle to control the user data in such “web applications”.

IMHO, he (probably unintentionally) forgot to mention one important question for me: will the user agree to let big companies manage/control/look at their (personal/private/whatever) data? And will the user still have the control of their own data?

First, imagine one day without internet connection? It could already be difficult now; it will be even more difficult when you’ll not be able to access your data (Firefox3 and its support for offline applications could be the beginning of a solution). Second, by putting your data in online applications like webmail, online wordprocessor, spreadsheet, etc., the user is giving these companies control over their data. Who read service, privacy and IP policies? Everyone should, nearly no one does (and GooDiff is there to help ;-)). Moreover, everything is free today (or advertisement-based, to be precise), will it still be free tomorrow? Will the features you enjoy today still be there in 1 or 2 years? Finally, in the off-line computer world, you are not locked-in anymore by big companies and proprietary file formats. While it is possible to save your data from big web applications on your hard disk (and sometimes in standardized formats), you are not able to easily/automatically retrieve your data from most of these “Web2.0” toys. I’ll end up this early post by a quotation from Peter Rip’s blog (emphasis is mine):

Much of the “easy” innovation seems to have been wrung out of the Web 2.0 wave. […] Now the hard work begins, again. The next wave of innovation isn’t going to be as easy. […] Now the hard part is moving from Web-as-Digital-Printing-Press to true Web-as-Platform. To make the Web a platform there has to [be] a level of content and services interoperability that really doesn’t exist today.

Noise level due to ventilation

Since a few days, I am back to my previous laboratory to collect some more samples. While looking after my rats, I measured the noise level with a dBmeter. The conditions are:

  • 8.30 am
  • doors are left open (except in the housing unit) as it is usually the case
  • five samples per room: one in each corner of the room (without moving any furniture) and one in the middle
  • measures taken at ear height
  • device: YF-20 (YFE)

noise level measures

The general mean is 61.7+/-3.3dB. But if we go into the details, a Kruskall-Wallis ANOVA shows most of the rooms have the same dB levels. But there is a significant statistical difference between the room where we perform experiments and the housing unit (p < 0.05). And there is a very significant statistical difference between the experiments room and the second office (p < 0.005). A significant statistical difference is also there between the two offices (p < 0.05; now guess in which one I am …).

Although very high compared to other labs, these levels are not considered as harmfull (same level as a busy restaurant – but you don’t stay 8hours a day in a restaurant). And anyway I am alway wearing ear plugs (3M 1100). On their box, it’s written they reduce noise level by 20-30dB.

Would you like to visit one of my lab?

It will be possible on this Saturday March 17th, 2007! For the EDAB Brain Awareness Week, one of my lab is organizing some conferences and you’ll also have the opportunity to visit the lab and see demonstrations on experiments we do and how we do. One of my mentors, Dr. P. Leprince, will tell (and show) you how we can identify proteins and identify their roles. Other workshops include microscopy, electrophysiology, behaviour. Conference topics include stem cells, drug addiction, injuries in the brain. You can have more info on the lab website (look for our activities, in French).

Unfortunately, I may not be there since I could have some experiment to do in the other lab, at the same time.

About iPod+DRM

I don’t understand why people are buying and offering Apple iPods to their family members. In fact, offering an iPod is like telling you: “Here is a costly electronic device I’m giving you, it’s cool thanks to huge marketing efforts but hey, in 5 – 10 years (or immediately if you lose your player), you won’t be able to read any music files you bought anymore: it has DRM inside. Moreover, when this one will be old, you’ll be forced to buy an Apple player to keep listening to music you bought”. In short: “I am offering you a beautiful trap”.

I recently bought a Samsung Flash player. It has a really nice design, it is easy to use, it behaves like any USB key (so you don’t need drivers, specific software, …) and, more importantly for me, it can play ogg vorbis files without any problem! 🙂

More info on this DRM-thing? Read the Stop DRM Now website (French equivalent), the Defective by design website and why DRM puts you at risk as innovator, artist and even consumer.

How do I handle my bibliographic data?

In science, you have to justify nearly all your assertions and this is done by citing another scientific paper, called a “reference”. With practise and advices of some people, I arrived to a satisfactory references management system I’ll explain below. My “problem” is that in the academic world where I work nearly everyone use EndNote or Reference Manager, two proprietary reference management software for MS-Windows. And I want to use the simple yet powerful BibTeX system.

I used both MS-Windows software and they all have advantages and drawbacks. Reference Manager has the nicest user interface but it lacks of support for other documents than MS-Word, RTF parsing and BibTex export. EndNote has an ugly and sometimes not logical UI but at least it has RTF document support (but nor OpenOffice nor Wordperfect documents are supported). With EndNote, you can find tricks on the web to import and export references from and to BibTeX. But you always lack something in the conversion. The reason is you have fields in EndNote that are not supported by standard BibTeX (this is not a problem since BibTeX simply ignore them without error but they are still available in your .bib file – you don’t loose any information) and fields in BibTeX that are not supported by EndNote (and EndNote simply discards them – you loose information).

I tried many other software, both free/open source and proprietary but I stay with my simple BibTeX file (simple, powerful, no additional markers, file not easily corrupted, small size, …). Maybe when the bibliographic project will be ready, I’ll try it.

In biology and medicine, the source/database of article references is PubMed. 99% of my references are first found on PubMed (the 1% left contains books, multimedia files and some articles not referenced on PubMed). Each reference is associated with a “PubMed ID” (PMID).

When an electronic version of an article is read, I change its file name following this convention: “first author’s name – last two digits of year – journal abbreviation – issue number – first page – some keywords” (without spaces nor punctuation marks, e.g. maquet01-science-294-1048-sleep-learning-memory.pdf). All the files are stored in the same directory. When a paper version of an article is read, I write keywords/tags on top of the first page and put the article in a file (each file has one subject ; it’s sometimes difficult to choose in which particular file an article should go).

Then I go to PubMed, find the PMID and look for this ID in both EndNote and PyP2B. I add the result of PyP2B in my BibTeX file with the keywords/tags ; this is simple (eveything is done by the script, even the key generation – I use something like “firstauthorsnameXX” where XX are the publication year last two digits). Since EndNote only understands reference numbers, I have to add the BibTeX key as a “label”. Fortunately, EndNote can sort references based on their labels. I also add a link to the PDF if it exists. I first thought that it will take me a lot of time to maintain these two lists of references but, practically, it doesn’t take much time.

With this system, I can:

  • look for a particular article in my server directory based on keywords/tags, first author, journal name and publication year
  • look for a particular reference in my BibTeX file
  • look for a particular reference in my EndNote files
  • use my BibTeX file in any LaTeX documents
  • use my EndNote files with MS-Word documents if someone ask for this type of document
  • 🙂

Previously, I had the project of writing a central repository of all the references in a real database and then generate both EndNote and BibTeX files from it. But I lack time to write this and EndNote file format is not open (why bother reading unofficial specifications about this format then?).

Receiving broken vials …

Antibodies vials inside the broken cool-packI was eager to receive some new antibodies for western blotting (I was waiting for them since December 2006!). They finally arrived on Wednesday but everything was broken inside! 😦 A plastic shell was supposed to protect the precious vials (about 300US$ each) but even that was broken. I immediately phoned the company and they promised me new vials for next Wednesday. Suddenly, it’s possible to get them in one week … Well, let’s see what I’ll get on that day …

A small journey in the world of LiveCDs

I have plenty of other things to do but, this evening, I decided to stop a little bit and try some LiveCDs I freely got at Fosdem. Since I did it very quickly and was tired, don’t take what I wrote for granted: LiveCDs are there to be tested. Download one and test it by yourself!

The first LiveCDs I tried were derived from Sun OpenSolaris (and on the OpenSolaris starter kit DVD). BeleniX was quite cute, directly launching XFCE. Quite a few applications were there. Some refresh problems were also present in the console. An old USB key was recognised without problem, as most parts of my low-end workstation.

click to enlarge the BeleniX screenshot

The next LiveCD was NexentaOS, aka GNU/OpenSolaris. It took so long to finally display a rather empty Gnome desktop. In fact, it took a long time to load anything, any application without any warning, indication, nothing. So I was left wondering if my machine had to be restarted or not. Since I also got a DBUS error, I was unable to use the USB key to save a screenshot but, since the network was detected, I was able to transfer the image on another computer. Not many applications were present. Quite disappointing.

click to enlarge the Nexenta screenshot

Finally, Schillix was quite strange because there were no X windowing system (apparently, they are currently trying to build a version of X). I don’t mind text-only operating system. But here, I had a sendmail error popping all the time. It was quite annoying. Finally, I didn’t get a good impression of OpenSolaris with all these LiveCDs. Anyway, OpenSolaris is not free (but only open source).

The next LiveCD was FreeSBIE and I really liked it. The desktop took a little long time to load (but at least I was able to see what’s happening on the screen). It also uses XFCE but it was very well designed, with what a geek wants on the top right corner 😉 I was also impressed by all the multimedia applications included (even Ekiga but I didn’t tested them since that computer is used for serious work and has no sound card). Maybe, one day, I’ll try to install a full BSD system …

click to enlarge the FreeSBIE screenshot

Finally, the last LiveCD I tested was Novell OpenSuSE. As usual with SuSE, you can count on a great design. I asked for a Live Gnome version. I just disliked the start menu “a la Vista”: you need 2 mouse-clics to have all the applications you can launch (see screenshot below). Moreover, when you get that screen, it starts with the A for Applications, a category that doesn’t contain the most useful applications (so you have to scroll down and/or click one more time to reach the app you want!).

click to enlarge the OpenSuSE screenshot

One final word: I didn’t talk about the common applications on these systems since you nearly get the same pieces of software on each of them (Firefox, OOo or AbiWord/Gnumeric/…, Thunderbird, etc.).