Month: July 2006

Dissatisfied with blog systems

Personnally, I am not very satisfied with current common blog systems. They are based on a huge collection of PHP scripts and MySQL but web providers couldn’t certify that service will have all the ressources needed. I am looking for something simpler, even if this solution is not (will not become) a major blog system …

Thanks to Google Cache, I was able to retrieve a nice idea Alexandre Dulaunoy had on his previous blog software (unfortunately, this idea was removed, along many others, when he changed for a new version of oddmuse). Here is the quote:

My (we)blog needs to be refreshed but I’m still looking for a simple free software to do the job. I tested various without finding a simple software backend. My requirements :

  • A vty (or at least an XML-RPC interface) interface to update the blog remotely
  • The software backend must be able to produce static pages without too much code or configuration
  • The ability to avoid spam in an efficient way (ok, the requirement moved to static pages, it would permit to avoid the spam problem 😉
  • The ability to customize the full look-and-feel of the blog via CSS. This seems pretty simple in theory but in practise, that’s another story.

At the end of the evaluation, I came with two possible software : Emacs Muse or Oddmuse wiki engine. I’m already using Oddmuse for my messy working place. I would be very happy to get any information about possible alternative.

Some comments:

  • With a VTY interface, one can directly connect from anywhere, via telnet or SSH. It is a good idea: the software is then simple, it can be accessed from anywhere (provided you have an access to your server or you have an always-on computer that can upload new posts on the real server).
  • I don’t see exactly what Alexandre wants with his XML-RPC interface since it is only a kind of remote procedure call. If I try to imagine what he meant, the software would then be different and you will need two of them: a client (where you write your new entry, answer to comments, etc.) and a server (that will receive a message containing your entry, parse it and publish it). Of course, you can have the same software package that provides both services: a VTY interface and a XML-RPC interface
  • If you are using VIm, here is another solution to Emacs Muse: vimblog 😉

My solution should then be this one … You simply write your entries with your favorite text editor and save it in an ad hoc directory. Every x minute/hour/day, a cron job launch the blog software. This simple software (C/Perl/Ruby/whatever) then parses the ad hoc directory. It finds small texts creation/modification date + time and rename files if needed (YYYYMMDDHHMMSS). There is a very small chance that two posts are posted at the very same second. Then it parses the files there for their content, build basic HTML files, apply a style (skeleton for HTML and CSS for style) and publish the pages to a FTP server. Plus an optional XML-RPC interface if you want.

For comments, a simple solution should be an e-mail address dedicated to the blog software. Comments are just texts sent to a special e-mail address. When the blog software runs, it also checks “its” mailbox, retrieve comments. Then, depending on the configuration, it could just append the comment to its initial post or it can ask the moderator for approval.

So, it’s not a common blog tool, i.e. it’s not web-based at all (although it could be possible to write a web interface if one whishes). It is especially well suited:

  • if you don’t care too much about your blog visual aspect (this point can be changed by adding new CSS);
  • if you have a website without PHP/MySQL and/or your website provider is too slow to process exhaustive, beautiful and huge blog engines
  • if you have access to console on a GNU/Linux computer but you don’t want to host your blog there (too little time for proper real world, secured servers configuration, not much bandwidth quota each months).

Someone to begin to code this with me?

Some thoughts about a family website

I am currently building a family website. Here are some requirements:

  1. services will be based on existing free software (I don’t have time to develop a complete solution)
  2. first service provided: a news service (I don’t know if it will be a forum or a shared blog)
  3. second service provided: a photo gallery
  4. all this should be on a shared host server (so it should work with PHP safe mode enabled ; I don’t have time to maintain a dedicated server)
  5. all this will allow everyone in the family to add elements, it will need very little maintenance and it should also be fast
  6. an e-mail address will be provided to everyone (all serious providers give e-mail addresses)

Although I am running WordPress for this blog, although a friend of mine is running DotClear, I am tempted to try b2evolution (blog), TextPattern (blog and more) or even Vanilla (forum) for the first service (blog). What is interesting is that these tools are localized in French, they allow multiple author to write and, finally, they have an anti-spam service “out-of-the-box”.

For the second service (photo gallery), I am tempted to use either LinPHA, PhpWebGallery or singapore.

I’ll dig a little bit more for more information … I’ll try to finish all this before Monday.

A first scientific paper from the Falisse-Poirrier!

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).

The "bioinformatic effort"

In the June 2006 issue of BioTechniques, Thomas Conrads and colleagues wrote an article about mass spectrometry used in biomarker discovery [1]. It is part of a “Special Section” devoted to mass spectrometry for proteomics analysis that is worth reading in itself. But one figure caught my attention. In this figure (reproduced below), they plot the mass spectrometry data acquisition effort and bioinformatic effort -vs- the experimental focus. In the few past years, people relied too much on the increasing power of mass spectrometry and bioinformatic tools in their experimental design. The authors criticise the fact that people “are overly dependent on technology and suffer from lack of imaginative sample preparation”. It’s not because analysis power is available downstream that sample collection and processing could be neglected.

Conrads'figure 1 about the importance of sample preparation
Reproduction of Conrads’figure 1

As shown in Figure 1, there is often an inverse relationship between the complexity of sample preparation and the amount of data acquired or the sophistication of the bioinformatic analysis. Simply put, minimal sample preparation prior to MS analysis will require more data acquisition and more sophisticated bioinformatic analysis. There is, however, a direct correlation between the amount of data acquired and the sophistication of the bioinformatic analysis.

Schematic protein identification process
Schematic protein identification process (for those who need it)

[1] T.P. Conrads, B.L. Hood and T.D. Veenstra. Sampling and analytical strategies for biomarker discovery using mass spectrometry. BioTechniques (June 2006) 40 (6): 799-805 (full text in html ; free registration required)

"Hacking the genome"

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)

Interesting interaction between videotracking and computer games

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 :

Bugs playing pacman with you

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
Tracking of a rat in the Morris water maze
rat = big, red spot on top
its trail from bottom is also in red

Next time, rats will solve crosswords …

rat solving crosswords

Some quotes …

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.) …

Many of the things I learned [at University] I never used in my professional life, but I guess it helped develop some of my axial lobes. I used those lobes to replace the lobes I lost due to the amount of alcohol we needed to wipe out after the exams.

I am so glad I am not doing astrophysics or particle physics, because what it actually means is that there are so many people involved in any experiment you are just a tooth in the wheel and, if you end up at the top of the food chain, it is more by luck than your abilities. Those at the top could just as well be journalists or politicians.

Many people chose a subject for their PhD and then continue the same subject until they retire. I despise this approach. I have changed my subject five times before I got my first tenured position and that helped me to learn different subjects.

Gecko tape was a sideline. I simply cannot keep to the same track in my research. It is very difficult to get research money for something new. You have to ask for money to continue something that is old, but I believe you should use some of the money to try something new.

When you have a thousand people researching one subject, they start acting like a single organism that acts by its own rules.