QSoas: frequently asked questions

Dynamique réactionnelle des enzymes rédox multicentres, cinétique électrochimique

Reaction dynamics of multicenter redox enzymes, electrochemical kinetics

Frequently asked questions

Help !

Where can I get help ?

First, try looking at the tutorial, peruse the FAQ and read the command reference. If that doesn’t solve your problems, you can post an “issue” on github, or contact us on twitter or Facebook.

I love QSoas ! How can I help ?

Thanks ! We love it too ! There are many things you can do to help the development of QSoas:

  • Report bugs or inaccuracies in the documentation to the github tracker.
  • Fix them ! You can fork the repository on github.
  • Ask for new features in the github tracker, and possibly write the code for them also !
  • Like us on Facebook, follow us on twitter.
  • Ask questions about your data analysis on github, twitter or Facebook. You can also use direct messages if you’d like to keep the question confidential.
  • Write about your own data analysis in QSoas.
  • And, most importantly, spread the word: show others how you did benefit from using QSoas !

Using QSoas

Why can’t I copy text from the terminal window ?

Keyboard shortcuts are disactivated in the terminal window (so that they always work in the command-line prompt), but if you select text in the terminal window and right-click on it, you’ll have the possibility to copy to the clipboard.

How can I save the data I have modified ?

Using the command save you can export data you have modified with QSoas. It saves the data as a TAB-separated text file. If you need to save many datasets in one go, have a look at save-datasets.

What is this output file thingy ?

Many commands of QSoas write information to a plain text file called the output file; this is for instance the case of the peak-detection commands (1 and others), reg, cu… The output file is created in the current directory the first time it is needed. It’s name is output.dat, but this can be changed using the output command. Format is TAB-separated, so you can import that into your favorite spreadsheet program, or even using QSoas itself (but you will probably have to pass the option /comment=# to load, and select the columns you’re interested in with /columns=...).

My output file looks all messed up, what happened ?

This is probably the result of you trying to modify the output file while QSoas is using it. Just don’t do that, or, if you absolutely need to, run the following command after saving your modifications from external programs to the output file:

QSoas> output /reopen=true

(this will only work with QSoas version 2.0 or later)

Display

My display looks all messed upand shows only points !

By default, QSoas shows datasets by drawing lines between all the successive points. On very noisy datasets, this sometimes leads to extremely long drawing times. QSoas detects this situation and replaces the drawing of lines by just dots. If you think QSoas got the heuristics wrong with your file, send us the data file.

I want to configure the color of the display !

As of now, QSoas does not support configuring fine details in the display. You can toggle the display of points using the points command, and you can use the /style= option to commands generating several datasets to use gradients to display a set of datasets.

File formats

Can QSoas read any file ?

No. But, it can read essentially all text files, which all data acquisition programs generate via their “export to ASCII” or “export to CSV”. QSoas should detect automatically the format of those files, but if it does not, have a look at the command load-as-text for specifying the details QSoas did not manage to guess, such as the column separator, the decimal separator.

I use GPES, can QSoas read the ixw (not oxw) file?

QSoas makes use of the information files generated by GPES (for chronoamperometry and cyclic voltammetry only, i.e. the .ixw and .icw files). See the data QSoas could find using the show command.

Can I use QSoas to read NOVA files?

NOVA produces large opaque binary files whose format is not public. This is the reason why QSoas cannot read them (although that may change if the format specs are published). If you want to process the data with QSoas (or any other software than NOVA !), you have to export the data to ASCII, either after the experiment, or even by including an “Export to ASCII” command in the experiment setup.

How can I load EC-Lab ASCII files

EC-Lab ASCII files are essentially semicolon-delimited CSV files. Look for a line in the spirit of

mode;error;time/s;Ewe/V

This shows that it is a data file, that is the 3rd column, and the 4th one, and that the separator is indeed ;. Try to load it using

l ocp_C02.csv /separator=; /columns=3,4

Don’t forget the /decimal=, option if you are using French decimal separator.

QSoas doesn’t read my files !

What if load a file and you don’t see anything at all, or data that really don’t look like yours ? QSoas tries to be smart and find under which format are stored data files, but it does not always guess right.

First, make sure the file data is a text file, i.e. open it with a text editor. If you see numbers that look like your data, it is a text file, if all you see is nonsensical symbols, what you have is a binary file. Go back to the software that produced it, reload it, and look for “Export as Text/ASCII” functions.

If you see the numbers, guess the structures: what is the decimal separator ? What is the column separator ? What are the columns you’re actually interested in ? The decimal separator can be set using the /decimal= option to load, the column separator using the /separator= option. You can specify the columns using the /columns= option. By default, load ignores lines that look like text – that don’t start with a number. You can turn that off by setting /comment=# (to only ignore lines that start with a #).

You can get an idea of how QSoas read the file by launching the edit command.

QSoas loads my file but doesn’t show anything

First of all, look at the data using edit, that shows a spreadsheet. You can then understand what exactly QSoas loaded.

Sometimes, data files contains lines of text at the beginning, which are sometimes by QSoas for real data lines. If that’s the case, the first few lines in edit would show entries with nan. To get rid of them, try:

QSoas> strip-if x.nan?||y.nan?

Fits

Can QSoas be used to fit a model that is calculated with an external program? Like EasySpin or Matlab?

This is not possible at the moment, but we have plans for a generic interface for using external programs to compute datasets. This would make it possible to fit using results of computations done within Matlab for instance, such as Easyspin. Let us know on the tracker if you’d like to do that.

How can I export “clean” version of the fit data ?

The simplest way is to use “Data…”/”Push current to stack” function from the fit window, that will push the simulated curve to the stack. You can save it later using the save command.

However, if you don’t have so many data points, but you would like to have a “smooth” curve nevertheless, save the fit parameters, generate a dataset with the desired range of values using generate-dataset, respawn the fit window, load the parameters and then export as before (“Data…”/”Push current to stack”).

My multi-fit is way too slow…

Fitting many datasets with parameters in common is quite an expensive task. At the beginning of the fit, QSoas writes the total number of free parameters for the fit. The time taken by the Levenberg-Marquardt algorithm used by most of the fit engines scales as the cube of the number of parameters, which in turns scales as the number of datasets in large multi-fits in which some parameters are dataset-specific. While this limitation cannot be overcome easily, we have developed a specific fit engine (called “Multi”) optimized for that kind of situation.

If you are fitting kinetics or redox titrations at many wavelengths (like in the tutorial), try reducing the number of wavelengths by applying downsample before running transpose.

Data analysis

How can I cut out data points from a dataset ?

Depends what you want to do. If you want to manually remove a few points, try deldp. If you want to cut out a whole segment, try rather cut, hitting the u key to keep what’s outside of the region instead of what’s inside. You can remove repeatedly segments with the r key in cut.

Another completely different approach is the use of strip-if, that removes data point that satisfy a condition. For instance, to remove all data points with negative values of y from a dataset, try:

QSoas> strip-if y<0

Copyright

I have just bought QSoas, can I give it to my friends? How do you expect to make money if the program is not protected?

QSoas is distributed under the GNU General Public license version 2.0, which means among other things that you can redistribute the binaries so long as you can provide the source code for them.

While you can get the binaries legally for free from a friend, think about it. Buying the fairly inexpensive binaries help the development of QSoas, and hence is a gift from you to the whole community of users of QSoas.

Why on earth do I have to pay for a free program ?

Well, you don’t have to pay. You can grab the source code from the download page and compile it from the source; actually this is the only supported way to get the program under Linux. However, if you want to be spared the hassle to compile the application yourself, you can buy the pre-built binaries, and feel good because you are contributing to the further development of QSoas !

Bugs, updates

I believe I found a bug, can I report it ? Can I get my money back?

The best way to report a bug is to signal it on the github tracker.

Please include all information necessary to reproduce the bug, such as what you exactly did, what you got, what you expected to get, the exact version of QSoas and the output on the terminal when applicable. If data confidentiality is not a problem, consider sending a binary stack saved using save-stack.

We don’t offer refunds – the license explicitly states that:

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE

However, if the information you provide us helps us identify and fix the bug, we’ll try to provide you with an updated version.

I have bought QSoas 1.0, will I need to pay again each time a new version is released?

You purchased a single binary. Later versions are not included in the price. Consider the price of QSoas: most of the softwares that are orders of magnitudes more expensive than QSoas do not include updates either in the purchasing cost. If that isn’t acceptable for you, you may consider compiling QSoas from source.

Why isn’t there a win64 binary version ? Will there ever be one ?

There are currently no plans for a win64 version. However, QSoas, like all other 32 bit applications, works seamlessly in 64 bit versions of Windows, thanks to the so-called WOW64 windows layer. The only drawback is that you cannot use more than 3GB or so of memory from QSoas, which should seldom be a limitation.

This file was written by Vincent Fourmond, and is copyright (c) 2014-2020 by CNRS/AMU.