Hi,
This interface looks awesome! Interestingly it looks quite similar to
another GUI attempt of mine back in 2002 that I called 'xmf' (relax
was originally called 'mf') with R1, R2, NOE, and model-free tabs on
the left hand side. That interface was a dead end though, unlike this
one. I think it would definitely benefit relax to have it
incorporated directly into the program! And might benefit you too as
many people would then have access and be able to improve the
interface (i.e. maybe useful for citation count). So if you would
like to jointly work with me to incorporate this code into relax
proper, that would be much appreciated.
relax has been specifically designed for handling multiple user
interfaces (UIs). Note that other people have plans for alternative
interfaces, more specifically the QT toolkit and the associated OpenGL
canvas for drawing. Therefore I would suggest the following, if you
would like to have this incorporated directly into relax. The first
would be to attach the code to a task that I will soon set up. I can
then also create a branch from the 1.3 line to incorporate the code.
For this, the code standards need to be quite high - as in most open
source projects - passing the validation script
'scripts/code_validator.py' and conforming to the conventions set out
in the development chapter. I can help a lot here. Then, as multiple
GUIs might exist in the future, I would suggest launching the
interface by typing something like:
$ relax --gui bieri
I would also set this as the default interface so that only:
$ relax --gui
needs to be typed. This can be aliased to:
$ relax -g
or maybe even:
$ relax -b
(for the Bieri interface). What do you think?
For the part where relaxGUI generates and executes a script, this
could be simplified. This essentially goes from the GUI interface to
the script interface in 'prompt' to the code in 'generic_fns' (and
sometimes 'specific_fns'). This is not necessary as the code in
'prompt' is only to check that the correct arguments have been
supplied in the script. Therefore what can be done is that the
'prompt/check.py' module can be used to check the values input through
the GUI, and then the 'generic_fns' and 'specific_fns' directly called
as illustarted in the code in 'prompt/'. This avoids the script and
runs relax directly, method by method. This should not require too
much work and will significantly increase the capabilities and power
of the GUI. The concept is illustrated in figure 9.1 of the relax
manual, "The core design of relax". This should also remove the parts
of the interface that make it GNU/Linux only, so it can then also run
on Mac OS X and MS Windows.
There is one problem which would need to be resolved. In the
model-free page, the Modelfree4 logo has been used. This will need to
be changed due to copyright issues. And because it is Art Palmer's
logo for his software (which is not recommended to be used due to the
issues mentioned in the 2 papers from 2008 "Optimisation of NMR
dynamic models I and II: ..." that I published with Paul Gooley).
relax can operate without Modelfree4 and should do so through a GUI.
As for a picture to use, I'm not sure. Maybe a picture of a protein
with model-free dynamics mapped onto the structure and the diffusion
tensor placed over the top? Though that is a bit boring. Do you have
any ideas?
Finally this should be published, just as FASTModelfree was!
FASTModelfree is just a basic GUI interfacing with Modelfree4, and
this GUI you have written appears to be much more advanced.
FASTModelfree was a JBNMR article, but this GUI could be published as
a communication to JACS or somewhere else. The FASTModelfree paper
reanalysed the RNA H data of Mandel et al., so maybe a reanalysis of
old data could be done for this publication? The Bacteriorhodopsin
fragment data of Orekhov et al., 1999 could be a useful target as I
used that in my 2008 back-to-back publications (and Orekhov did the
analysis really well, and correctly, on a very difficult system).
Cheers,
Edward
2009/11/11 Michael Bieri <michael.bieri@xxxxxx>:
Hi
I wrote a graphical user interface for relax and Edward suggested to discuss
this in here. Attached are screen shots of the program.
It is designed to enable simple model-free analysis by drag-and-drop or
browsing of the peak files. It works with up to three different magnetic
fields. Results generated by relaxGUI are listed in a separate tab and can
be observed. Furthermore, relaxGUI gives a feedback if the relax run was
successful or not. Model-free calculation can be executed either active or
in the background.
The program actually creates and runs scripts in relax. I tested it on
Ubuntu 9.10 using relax 1.3.4. The program is written in python and uses
wx.Python for the GUI.
As told by Edward, the program will be uploaded as a task.
Cheers
Michael
--
Michael Bieri, PhD
Department of Biochemistry and Molecular Biology
Bio21 Molecular Science and Biotechnology Institute
The University of Melbourne, 30 Flemington Road
Parkville, Victoria 3010, Australia
Tel.: +61 3 8334 2256
http://www.biochemistry.unimelb.edu.au
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Re: GUI for relax