The purpose of this post is to demonstrate a first approach to the analysis of multiwavelength kinetic data, like those obtained using stopped-flow data. To practice, we will use data that were acquired during the stopped flow practicals of the MetBio summer school from the FrenchBIC. During the practicals, the student monitored the reaction of myoglobin (in its Fe(III) state) with azide, which yields a fast and strong change in the absorbance spectrum of the protein, which was monitored using a diode array. The data is publicly available on zenodo. Aims of this tutorial The purpose of this tutorial is to teach you to use the free softwareQSoas to run a simple, multiwavelength exponential fit on the data, and to look at the results. This is not a kinetics lecture, so that it will not go in depth about the use of the exponential fit and its meaning. Getting started: loading the file First, make sure you have a working version of QSoas, you can download them (for free) there. Then download the data files from zenodo. We will work only on the data file Azide-1.25mm_001.dat, but of course, the purpose of this tutorial is to enable you to work on all of them. The data files contain the time evolution of the absorbance for all wavelengths, in a matrix format, in which each row correpond to a time point and each column to a wavelength. Start QSoas, and launch the command:

QSoas> load /comments='"'

Then, choose the Azide-1.25mm_001.dat data file. This should bring up a horizontal red line at the bottom of the data display, with X values between about 0 and 2.5. If you zoom on the red line with the mouse wheel, you'll realize it is data. The /comments='"' part is very important since it allows the extraction of the wavelength from the data. We will look at what it means another day. At this stage, you can look at the loaded data using the command:

QSoas> edit

You should have a window looking like this: The rows each correspond to a data point displayed on the window below. The first column correspond to the X values, the second the Y values, and all the other ones to extra Y columns (they are not displayed by default). What is especially interesting is the first row, which contains a nan as the X value and what is obviously the wavelength for all the Y values. To tell that QSoas should take this line as the wavelength (which will be the perpendicular coordinate, the coordinate of the other direction of the matrix), first close the edit window and run:

QSoas> set-perp /from-row=0

Splitting and fitting Now, we have a single dataset containing a lot of Y columns. We want to fit all of them simultaneously with a (mono) exponential fit. For that, we first need to split the big matrix into a series of X,Y datasets (because fitting only works on the first Y). This is possible by running:

QSoas> expand /style=red-to-blue /flags=kinetics

Your screen should now look like this: You're looking at the kinetics at all wavelengths at the same time (this may take some time to display on your computer, it is after all a rather large number of data points). The /style=red-to-blue is not strictly necessary, but it gives the red to blue color gradient which makes things easier to look at (and cooler !). The /flags=kinetics is there to attach a label (a flag) to the newly created datasets so we can easily manipulate all of them at the same time. Then it's time to fit, with the following command:

QSoas> mfit-exponential-decay flagged:kinetics

This should bring up a new window. After resizing it, you should have something that looks like this: The bottom of the fit window is taken by the parameters, each with two checkboxes on the right to set them fixed (i.e. not determined by the fitting mechanism) and/or global (i.e. with a single value for all the datasets, here all the wavelengths). The top shows the current dataset along with the corresponding fit (in green), and, below, the residuals. You can change the dataset by clicking on the horizontal arrows or using Ctrl+PgUp or Ctrl+PgDown (keep holding it to scan fast). See the Z = 728.15 showing that QSoas has recognized that the currently displayed dataset corresponds to the wavelength 728.15. The equation fitted to the data is: $$y(x) = A_\infty + A_1 \times \exp -(x - x_0)/\tau_1$$ In this case, while the \(A_1\) and \(A_\infty\) parameters clearly depend on the wavelength, the time constant of evolution should be independent of wavelength (the process happens at a certain rate regardless of the wavelength we're analyzing), so that the \(\tau_1\) parameter should be common for all the datasets/wavelengths. Just click on the global checkbox at the right of the tau_1 parameter, make sure it is checked, and hit the Fit button... The fit should not take long (less than a minute), and then you end up with the results of the fits: all the parameters. The best way to look at the non global parameters like \(A_1\) and \(A_\infty\) is to use the Show Parameters item from the Parameters menu. Using it and clicking on A_inf too should give you a display like this one: The A_inf parameter corresponds to the spectum at infinite time (of azide-bound heme), while the A_1 parameter corresponds to the difference spectrum between the initial (azide-free) and final (azide-bound) states. Now, the fit is finished, you can save the parameters if you want to reload them in a later fit by using the Parameters/Save menu item or export them in a form more suitable for plotting using Parameters/Export (although QSoas can also display and the parameters saved using Save). This concludes this first approach to fitting the data. What you can do is

• look at the depence of the tau_1 parameter as a function of the azide concentration;
• try fitting more than one exponential, using for instance:

  QSoas> mfit-exponential-decay /exponentials=2 flagged:kinetics
  

How to read the code above All the lines starting by QSoas> in the code areas above are meant to be typed into the QSoas command line (at the bottom of the window), and started by pressing enter at the end. You must remove the QSoas> bit. The other lines (when applicable) show you the response of QSoas, in the terminal just above the command-line. You may want to play with the QSoas tutorial to learn more about how to interact with QSoas. About QSoas QSoas is a powerful open source data analysis program that focuses on flexibility and powerful fitting capacities. It is released under the GNU General Public License. It is described in Fourmond, Anal. Chem., 2016, 88 (10), pp 5050 5052. Current version is 3.1. You can freely (and at no cost) download its source code or precompiled versions for MacOS and Windows there. Alternatively, you can clone from the GitHub repository.
Contact: find my email address there, or contact me on LinkedIn.

My recent rack design turned out to simply not be practical. It did not hold all the SBC I needed it to and most troubling accessing connectors was impractical. I was forced to remove the enclosure from the rack and go back to piles of SBC on a shelf.

This sent me back to the beginning of the design process. The requirement for easy access to connectors had been compromised on in my first solution because I wanted a compact 1U size. This time I returned to my initial toast rack layout but retaining the SBC inside their clip cases.

By facing the connectors downwards and providing basic cable management the design should be much more practical.

My design process is to use the QCAD package to create layered 2D outlines which are then converted from DXF into toolpaths with Lasercut CAM software. The toolpaths are then uploaded to the laser cutter directly from the PC running Lasercut.

Despite the laser cutters being professional grade systems the Lasercut software is a continuous cause of issues for many users, it is the only closed source piece of software in the production process and it has a pretty poor user interface. On this occasion my main issue with it was my design was quite large at 700mm by 400mm which caused the software to crash repeatedly. I broke the design down into two halves and this allowed me to continue.

Once I defeated the software the design was laser cut from 3mm clear extruded acrylic. The assembled is secured with 72 off M3 nuts and bolts. The resulting construction is very strong and probably contains much more material than necessary.

One interesting thing I discovered is that in going from a 1U enclosure holding 5 units to a 2U design holding 11 units I had increased the final weight from 320g to 980g and when all 11 SBC are installed that goes up to a whopping 2300g. Fortunately this is within the mechanical capabilities of the material but it is the heaviest thing I have ever constructed from 3mm acrylic.

Once installed in the rack with all SBC inserted and connected this finally actually works and provides a practical solution. The self is finally clear of SBC and has enough space for all the other systems I need to accommodate for various projects.

As usual the design files are all freely available though I really cannot see anyone else needing to replicate this.

The following contributors got their Debian Developer accounts in the last two months:

• Gianfranco Costamagna (locutusofborg)
• Graham Inggs (ginggs)
• Ximin Luo (infinity0)
• Christian Kastner (ckk)
• Tianon Gravi (tianon)
• Iain R. Learmonth (irl)
• Laura Arjona Reina (larjona)

The following contributors were added as Debian Maintainers in the last two months:

• Senthil Kumaran
• Riley Baird
• Robie Basak
• Alex Muntada
• Johan Van de Wauw
• Benjamin Barenblat
• Paul Novotny
• Jose Luis Rivero
• Chris Knadle
• Lennart Weller

Congratulations!

In light of the fact that it seems possible to fit the plastic caps of a Debian branded Swiss Army Knife (Last orders today!) on an existing Swiss Army Knife (German written howto as PDF), I started to think about which Victorinox Cybertool would be the best fitting for me. And because the Victorinox comparison page doesn t really show diffs, just columns with floating text which are not very helpful for generating diffs in your head, I used command line tools for that purpose: wdiff Because the floating texts are not line- but just whitespace-based, the tool of choice is not diff but wdiff, a word-based diff. It encloses additions and removals in + + and [- -] blocks. (No, those aren t Japanese smileys although they look a lot like some. ^^). The easiest and clearest way is to copy and paste the texts from Victorinox comparison page into some text files and compare them with wdiff:

$ wdiff cybertool34.txt cybertool41.txt
+Schraubendreher 2.5mm,+ Pinzette, N hahle mit Nadel hr, +Holzs ge,+ Bit-Schl ssel( 5 mm Innensechskant f r die D-SUB Steckverbinder, 4 mm Innensechskant f r Bits, Bit Phillips 0, Bit Phillips 1, Bit-Schlitzschrauben 4 mm, Bit Phillips 2, Bit Hex 4 mm, Bit Torx 8, Bit Torx 10, Bit Torx 15 ), Kombizange( H lsenpresser, Drahtschneider ), Stech-Bohrahle, Kugelschreiber( auch zum DIP-Switch verstellen ), Mehrzweckhaken (Pakettr ger), +Metalls ge( Metallfeile, Nagelfeile, Nagelreiniger ),+ Dosen ffner( kleiner Schraubendreher ), Kleine Klinge, Grosse Klinge, Ring, inox, Mini-Schraubendreher, Kapselheber( Schraubendreher, Drahtabisolierer ), +Holzmeissel / Schaber,+ Bit-Halter, Stecknadel, inox, Schere, Korkenzieher, Zahnstocher

So this already extracted the information which are the seven tools which are in the Cybertool 41, but not in the Cybertool 34. Nevertheless the diff is still not easily recognizable on the first glance. There are several ways to help here. First wdiff has an option --no-common (the according short option is -3) which just shows added and removed words:

$ wdiff -3 cybertool34.txt cybertool41.txt
======================================================================
 +Schraubendreher 2.5mm,+ 
======================================================================
  +Holzs ge,+ 
======================================================================
  +Metalls ge( Metallfeile, Nagelfeile, Nagelreiniger ),+ 
======================================================================
  +Holzmeissel / Schaber,+ 
======================================================================

This is already way better to quickly recognize the actual differences. But if you still also want to see the common tools of the two knifes you need some visual help: One option is to use wdiff s --terminal (or short -t) option. Added words are then displayed inverse and removed words are shown underlined (background and foreground colors hardcoded as there is no invert colors style in CSS or HTML):

$ wdiff -t cybertool34.txt cybertool41.txt
Schraubendreher 2.5mm, Pinzette, N hahle mit Nadel hr, Holzs ge, Bit-Schl ssel( 5 mm Innensechskant f r die D-SUB Steckverbinder, 4 mm Innensechskant f r Bits, Bit Phillips 0, Bit Phillips 1, Bit-Schlitzschrauben 4 mm, Bit Phillips 2, Bit Hex 4 mm, Bit Torx 8, Bit Torx 10, Bit Torx 15 ), Kombizange( H lsenpresser, Drahtschneider ), Stech-Bohrahle, Kugelschreiber( auch zum DIP-Switch verstellen ), Mehrzweckhaken (Pakettr ger), Metalls ge( Metallfeile, Nagelfeile, Nagelreiniger ), Dosen ffner( kleiner Schraubendreher ), Kleine Klinge, Druckkugelschreiber, Grosse Klinge, Ring, inox, Mini-Schraubendreher, Kapselheber( Schraubendreher, Drahtabisolierer ), Holzmeissel / Schaber, Bit-Halter, Stecknadel, inox, Schere, Korkenzieher, Zahnstocher

But some still like to to use color instead of the contrast-rich inverse and the easily to oversee underlining. This is where colordiff comes into play: colordiff colordiff is like syntax highlighting for diffs on the command line. I works with classic and unified diffs as well as with wdiffs and debdiffs (the debdiff command is part of the devscripts package).

$ wdiff cybertool34.txt cybertool41.txt colordiff
+Schraubendreher 2.5mm,+ Pinzette, N hahle mit Nadel hr, +Holzs ge,+ Bit-Schl ssel( 5 mm Innensechskant f r die D-SUB Steckverbinder, 4 mm Innensechskant f r Bits, Bit Phillips 0, Bit Phillips 1, Bit-Schlitzschrauben 4 mm, Bit Phillips 2, Bit Hex 4 mm, Bit Torx 8, Bit Torx 10, Bit Torx 15 ), Kombizange( H lsenpresser, Drahtschneider ), Stech-Bohrahle, Kugelschreiber( auch zum DIP-Switch verstellen ), Mehrzweckhaken (Pakettr ger), +Metalls ge( Metallfeile, Nagelfeile, Nagelreiniger ),+ Dosen ffner( kleiner Schraubendreher ), Kleine Klinge, Grosse Klinge, Ring, inox, Mini-Schraubendreher, Kapselheber( Schraubendreher, Drahtabisolierer ), +Holzmeissel / Schaber,+ Bit-Halter, Stecknadel, inox, Schere, Korkenzieher, Zahnstocher $ wdiff cybertool29.txt cybertool41.txt colordiff
+Schraubendreher 2.5mm,+ Pinzette, N hahle mit Nadel hr, +Holzs ge,+ Bit-Schl ssel( 5 mm Innensechskant f r die D-SUB Steckverbinder, 4 mm Innensechskant f r Bits, Bit Phillips 0, Bit Phillips 1, Bit-Schlitzschrauben 4 mm, Bit Phillips 2, Bit Hex 4 mm, Bit Torx 8, Bit Torx 10, Bit Torx 15 ), +Kombizange( H lsenpresser, Drahtschneider ),+ Stech-Bohrahle, +Kugelschreiber( auch zum DIP-Switch verstellen ), Mehrzweckhaken (Pakettr ger), Metalls ge( Metallfeile, Nagelfeile, Nagelreiniger ),+ Dosen ffner( kleiner Schraubendreher ), Kleine Klinge, [-Druckkugelschreiber,-] Grosse Klinge, Ring, inox, Mini-Schraubendreher, Kapselheber( Schraubendreher, Drahtabisolierer ), +Holzmeissel / Schaber,+ Bit-Halter, Stecknadel, inox, +Schere,+ Korkenzieher, Zahnstocher

(Coloured Screenshots done with ANSI HTML Adapter from the package aha.) Some, especially those who are used to git, are probably confused by the default choice of diff colors. This is easily fixable by writing the following into you ~/.colordiffrc:

newtext=green
oldtext=red
diffstuff=darkblue
cvsstuff=darkyellow

(See also /etc/colordiff for the defaults and hints.) colordiff has by the way two operating modes:

• Without parameter it reads diffs from standard input as seen above.
• With parameters it works as drop-in diff replacement including all diff options as shown below.

So now let us compare the Cybertool 29 with Cybertool 34 in a normal diff (by using the texts from above and replacing all commata with newline characters) with git-like colors:

$ colordiff cybertool29-lines.txt cybertool34-lines.txt
12a13,14
> Kombizange( H lsenpresser
> Drahtschneider )
13a16,17
> Kugelschreiber( auch zum DIP-Switch verstellen )
> Mehrzweckhaken (Pakettr ger)
16d19
< Druckkugelschreiber
25a29
> Schere

Or as unifed diff with some context:

$ colordiff -u cybertool29-lines.txt cybertool34-lines.txt
--- cybertool29-lines.txt     2011-08-31 20:55:37.195546238 +0200
+++ cybertool34-lines.txt   2011-08-31 20:55:11.667710504 +0200
@@ -10,10 +10,13 @@
 Bit Torx 8
 Bit Torx 10
 Bit Torx 15 )
+Kombizange( H lsenpresser
+Drahtschneider )
 Stech-Bohrahle
+Kugelschreiber( auch zum DIP-Switch verstellen )
+Mehrzweckhaken (Pakettr ger)
 Dosen ffner( kleiner Schraubendreher )
 Kleine Klinge
-Druckkugelschreiber
 Grosse Klinge
 Ring
 inox
@@ -23,5 +26,6 @@
 Bit-Halter
 Stecknadel
 inox
+Schere
 Korkenzieher
 Zahnstocher

So if you want nicely colored diffs with Subversion like you re used to with git, you can use svn diff colordiff.

Recently I blogged a serious complain about Facebook marketing practices.
I must note, that, while writing this, this is still a standing fact.
And it somehow leads me to the question why I use facebook (and similar portals like Xing or Meinvz at all) at all.

I would say that I'm a person, who values security. Probably I need to, because my job involves security aspects, even if its only to protect data.
Additionally I value privacy. I would never go onto a toilet in a glass case, where everybody could watch me doing my business.
The idea to keep the door to my flat open all the time would trigger all alarm bells inside of me.
But on the other hand I have a blog on which I write about technical topics, and personal topics. Like the death of my grandma or how my neighbours disturb me. And I use Facebook. And MeinVZ.

I'm well aware of how this makes it easier to trace me. How this could be used against me, if I happen to search for a job. Aware of the everlasting memorization of the internet who will keep this.. eventually forever.
And I have friends who have a serious antipathy against this and probably would never use such a portal at all.
So why do I use it?

That I started using that portals were some kind of peer pressure. I'm a person who likes beeing "thereby" and I like beeing present. Many of my friends were already using those portals and so I followed an invitation to use it, too. But I did think about several points:

• Could this affect my career plans? The answer is yes. But it can have positive and negative aspects. I'm active in the Open Source movement. Therefore I am already present in the world wide web. As an IT-guy that s not the worst that can happen. If you are interested in working for one of those big prominent companies and if its only peripheral, being present in the web is a good thing, because there is a chance of being perceived. On the other hand I'm a somehow crazy person in my private life. I like doing party and some people would probably call me freaky. Most likely this could show in such a portal.. or in my blog. If it affects my carrier plans in a negative manner, well there are several things to consider. For example if I really want to work for a company, which decides to decline me just because I have a real life next to the job. I probably don't.
• Can these portals store information about me that I don't want to be public?Yes and no. Its a fact that these portals are designed to collect as many information about as many persons as possible. But they also give you some tools to control what is known about you. If you don't want to show nude photos, then don't post them. If you don't want to be seen as a person always drinking too much then don't write about it and don't show photos of you being drunk. And if others post such stuff about you: Use the tools to get it removed and eventually ask yourself if the persons doing it are really friends.
• Are the companies behind those portals evil?Hard question. In many ways they are acting in a way that makes them look evil. Like that aggresive advertising, I wrote about earlier. But on the other hand they are serving a need of people who like to keep in touch and they are really just doing business. What they do is required for their business. They collect data because they need it to make their free portals financable (e.g. by showing targeted advertising). If you want you can still think of them as the great evil but you are not really being forced to use their service.
• Is every facebook friend a friend?Uhm.. no. Its so easy to request friendship on a social network platform that people collect "friends" on them as other people collect knickknack.
  Personally I consider my friend list on these portals to be a collection of people I know. Some of them are friends but not all of them.
• Do I really need those social networking platforms?And here is the most important question. The answer is No.
  No one does. If you really want to keep in touch with persons you like you can always do. By telephone, by writing a letter, by visiting them etc.
  But its convenient. An example:
  I have friends in different parts of the world. In the United States for example. Or people living in my country (but in a distance) or people travelling around a lot. I can keep in touch with them via email or instant messenging etc. but those social networks give me the chance to keep up-to-date with their lifes (in which I'm really interested if they are friends) without direct contact the whole time (for which we may not always find time and occasion). Its easy, its fast.

I came to the conclusion that there are pros and cons for and against using these services. And I found that I can live with the cons due to the convenience they bring to me. And that I could always stop using them.

However: That does not mean that I have to "Eat or die" what they serve.

Oh and on a side note: I found "Facebook, Br ste und die Currywurst" to be an interesting article about the topic. Its a recommended reading, although only for the people who understand German.

Ok, for some time now, I've been using my old Samsung Vm8100KXDT Laptop to connect my wired network to my Linksys WRT54GS router, which resides on another floor.

Well, if you read my old Drupal blog, you may have noticed, that I complained several times about my Netgear WG311T PCI card, being not able to be run in my PowerPCs. That's the reason why my Laptop was acting as a wired/wireless bridge (or more exactly a router between both worlds).

Today I bought a Linksys WET54G wireless bridge to replace my Laptop for that purpose. My Laptop was just too noisy and too power consuming and - even worse - the harddisk began to die. It was giving loud klackklack noises from time to time, resulting in a loss of DMA and therefore needed a power cycle afterwards.

Anyway, the WET54G is a nice small box with one antenna and one ethernet port. It is advertised as being a operating system independent device - which is clearly not true. You'll need a Windows PC to configure the device and it's quite awful to configure.

Instead of accessing the WET54G bei http, the CD-Rom contains a small program that scans the ethernet for that device. Next problem will arise when you want to configure your WLAN/WiFi settings. It is pre-configured to use channel 6 and infrastructure mode. Unfortunately, you'll need to first configure infrastructure or ad-hoc mode before you proceed to configure your ESSID, channel and b/g/mixed mode settings. Even worse because you can't change the channel or the mode when you have chosen infrastructure mode.

So in order to change your channel, you'll need to configure it in ad-hoc mode first, then change your channel and mode first, safe your settings, let the device reboot and continue with configuring infrastructure mode again.
Really badly tested piece of software, Linksys!

But beside of this huge annoyance the WET54G works quite nice once setup properly. Alas, I can't recommend it to buy for the above reasons.

Update:
After configuring it the first time, there actually is a webinterface, where you can configure the device with your favorite free OS. However, it was not accessible the first time to me, although I configured a Laptop to use the described default network in the manual. The above mentioned problems of not being able to configure the channel in infrastructure mode still exists in the webinterface.