A blog from a scientist and former Debian developer (and occasional book writer)... Tricks for data handling, programming, debian administration and development, command-line and many other joyful things in the same spirit. Oh, and sometimes completely unrelated things !
Version 3.3 brings in new features, including reverse Laplace transforms and fits, pH fits, commands for picking points from a dataset, averaging points with the same X value, or perform singular value decomposition. In addition to these new features, many previous commands were improved, like the addition of a bandcut filter in FFT filtering, better handling of the loading of files produced by…
Version 3.2 of QSoas is out ! It is mostly a bug-fix release, fixing the computation mistake found in the eecr-relay wave shape fit, see the correction to our initial article in JACS . We strongly encourage all the users of the eecr-relay wave shape fit to upgrade, and, unfortunately, refit previously fitted data as the results might change. The other wave shape fits are not affected by the issue.…
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…
The new version of QSoas has just been released ! It brings in a host of new features, as the releases before, but maybe the most important change is the following... Binary images now freely available ! Starting from now, all the binary images for the new versions of QSoas will freely available from the download page . You can download the precompiled versions of QSoas for MacOS or windows. So…
For the past years, most of the development has happened behind the scene in a private repository, and the code has appeared in the public repository only a couple of months before the release, in the release branch. I have now decided to publish the current code of QSoas in the github repository (in the public branch). This way, you can follow and use all the good things that were developed since…
This post describes two similar solutions to the Quiz #2 , using the data files found there . The two solutions described here rely on split-on-values . The first solution is the one that came naturally to me, and is by far the most general and extensible, but the second one is shorter, and doesn't require external script files. Solution #1 The key to both solution is to separate the original data…
This second quiz may sound like the first one , but in fact, the approach used is completely different. The point is to gather some elementary statistics from a series of experiments performed under different conditions, but with several repeats at the same conditions. Quiz You are given a file (which you can download there ) that contains a series of pH value data: the X column is the pH, the Y…
Redox-dependent inactivations are actually rather common in the field of metalloenzymes, and electrochemistry can be an extremely powerful tool to study them, providing one can analyze the data quantitatively. The point of this point is to teach the reader how to do so using QSoas . For more general information about redox inactivations and how to study them using electrochemical techniques, the…
I've decided to post regular summaries of all the articles written here about QSoas; this is the first post of this kind. All the articles related to QSoas can be found here also. The articles written here can be separated into several categories. Tutorials to analyze real data These are posts about how to reproduce the data analysis of published articles, including links to the original data so…
It is one thing to acquire and process data, but the data themselves are most often useless without the context , the conditions in which the experiments were made. These additional informations can be called meta-data . In a previous post , we have already described how one can set meta-data to data that are already loaded, and how one can make use of them. QSoas is already able to figure out…
First of all, let me all wish you a happy new year, with all my wishes of health and succes. I sincerely hope this year will be simpler for most people as last year ! For the first post of the year, I wanted to show you how to take advantage of Ruby , the programming language embedded in QSoas , to make various things, like: creating a column with the sum of Y values; extending values that are…
After almost two years of development, version 3.0 of QSoas is finally out ! It brings in a number of new features. An expert mode for fitting Undoubtedly the most important feature in the new version is a complete upgrade of the fit system, which now features an expert mode, turned on by using the /expert=true option with the fit commands. The expert mode features a command prompt that looks like…
By essence, QSoas works with \(y = f(x)\) datasets. However, in practice, when working with experimental data (or data generated from simulations), one has often more than one experimental parameter (\(x\)). For instance, one could record series of spectra (\(A = f(\lambda)\)) for different pH values, so that the absorbance is in fact a function of both the pH and \(\lambda\). QSoas has different…
This post describes the solution to the Quiz #1 , based on the files found there . The point is to produce both the average and the standard deviation of a series of spectra. Below is how the final averaged spectra shoud look like: I will present here two different solutions. Solution 1: using the definition of standard deviation There is a simple solution using the definition of the standard…
Often, one would want to generate smooth data from a fit over a small number of data points. For an example, take the data in the following file . It contains (fake) experimental data points that obey to Michaelis-Menten kinetics: $$v = \frac{v_m}{1 + K_m/s}$$ in which \(v\) is the measured rate (the y values of the data), \(s\) the concentration of substrate (the x values of the data), \(v_m\)…
Here is the first QSoas quiz ! I recently measured several identical spectra in a row to evaluate the noise of the setup, and so I wanted to average all the spectra and also determine the standard deviation in the absorbances. Averaging the spectra can simply be done taking advantage of the average command: QSoas> load Spectrum*.dat /flags=spectra QSoas> average flagged:spectra However, average…
This is the first post of a series in which we will provide the readers with simple tutorial approaches to reproduce the data analysis of some of our published papers. All our data analysis is performed using QSoas . Today, we will show you how to analyze the experiments we used to characterize the behaviour of an enzyme, the Nickel-Iron CO dehydrogenase IV from Carboxytothermus hydrogenoformans .…
The new release of QSoas is finally ready ! It brings in a lot of new features and improvements, notably greatly improved memory use for massive multifits, a fit for linear (in)activation processes (the one we used in Fourmond et al , Nature Chemistry 2014 ), a new way to transform "numbers" like peak position or stats into new datasets and even SVG output ! Following popular demand, it also…
QSoas can read and execute Ruby code directly, while reading command files, or even at the command prompt. For that, just write plain Ruby code inside a ruby ... ruby end block. Probably the most useful possibility is to define elaborated functions directly from within QSoas , or, preferable, from within a script; this is an alternative to defining a function in a completely separated Ruby-only…
I was recently looking for a way to extract many attachments from a series of emails. I first had a look at the AttachmentExtractor thunderbird plugin, but it seems very old and not maintained anymore. So I've come up with another very simple solution that also works with any other mail client. Just copy all the mails you want to extract attachments from to a single (temporary) mail folder, find…
Six month ago, I wrote a lengthy post about my new computer hurting my eyes. I haven't made any progress with that, but I've accidentally upgraded my work computer from Kernel 4.4 to 4.8 and the nvidia drivers from 340.96-4 to 375.66-2. Well, my work computer now hurts, I've switched back to the previous kernel and drivers, I hope it'll be back to normal. Any ideas of something specific that…
QSoas can run scripts, and, since version 2.0, it can be run completely without user interaction from the command-line (though an interface may be briefly displayed). This possibility relies on the following command-line options : --run , which runs the command given on the command-line; --exit-after-running , which closes automatically QSoas after all the commands specified by --run were run;…
I created some time ago a utils repository on github to publish miscellaneous scripts, but it's only recently that I have started to really populate it. One of my recent work is make-theme-image script, that downloads an icon them package, grabs relevant, user-specifiable, icons, and arrange them in a neat montage. The images displayed are the results of running ~ make-theme-image gnome-icon-theme…
I have been using almost compulsively ls -lrt for a long time now. As per the ls man page , this command lists the files of the current directory, with the latest files at the end, so that they are the ones that show up just above your next command-line. This is very convenient to work with, hmmm, not-so-well-organized directories, because it just shows what you're working on, and you can safely…
While the main focus of QSoas is the processing of experimental data, it also features commands to generate (calculate) datasets. The command generate-buffer creates a dataset of equally spaced points (you can change their number using the option /samples ) between to limiting values, as below: QSoas> generate-buffer -2 2 By default, the values are taken equal to . However, generate-buffer also…