Dynamique réactionnelle des enzymes rédox multicentres, cinétique électrochimiqueReaction dynamics of multicenter redox enzymes, electrochemical kinetics
Frequently asked questions
Where can I get help ?
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 !
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 ?
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
1 and others),
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
load, and select the columns you’re interested in with
My output file looks all messed up, what happened ?
This is probably the result of you trying to modify the output file
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)
My display looks all messed upand shows only points !
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
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
command, and you can use the
/style= option to commands generating
several datasets to use gradients to
display a set of datasets.
I want to make figures with QSoas
The current public version does not support to make figures, although
it is possible to save a PDF file using
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
.icw files). See the data QSoas could find using the
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
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
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
/comment=# (to only ignore lines that start with a
You can get an idea of how
QSoas read the file by launching the
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?
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
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.
How can I cut out data points from a dataset ?
Depends what you want to do. If you want to manually remove a few
deldp. If you want to cut out a whole segment, try
cut, hitting the
u key to keep what’s outside of the
region instead of what’s inside. You can remove repeatedly segments
r key in cut.
Another completely different approach is the use of
that removes data point that satisfy a condition. For instance, to
remove all data points with negative values of
y from a dataset,
QSoas> strip-if y<0
I believe I found a bug, can I report it ?
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
This file was written by Vincent Fourmond, and is copyright (c) 2014-2023 by CNRS/AMU.