Re: Consistency tests -- June 27, 2007

Hi,

Thanks !
It's fun to know that my efforts are appreciated..!

Let me know if something was wrong...

Maybe my name on the code headers should be modified to add the names of
the people who originally wrote the files in Jw mapping code (since I
mostly started by copying the code and modifying it).

Cheers


Séb



Edward d'Auvergne wrote:

Hi,

This is an awesome effort!  The best part is that this code doesn't
break any other parts of relax!  The code looks like it meets all of
relax's conventions perfectly (although there was maybe one or two
functions without docstrings).  There is also a few bugs that I have
noticed that will need to be sorted out (indecies of 1 in three spots
where they should be different, I can't remember the file off the top
of my head).

Because of the size of this patch, please allow me time to sort
through it all.  The norm is that large patches, such as this one, are
very difficult to have incorporated into an open source projects.  It
helps for code acceptance to discuss and develop the code in the
public eye.  However in this case, the code implements a new analysis
type and sits nicely alongside the rest of relax without modifying the
current code base too much (actually in this case barely at all).  The
code will need work prior to acceptance (like the sample script
including functions to create the output graphs) but it could be that
the code is so well-behaved that it could make it into the 1.2 line.
Nevertheless it will need to be added to the 1.3 line for it to exist
within future relax versions.  Thank you for this great effort.

Cheers,

Edward



On 6/26/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:

Hi,

I started working on implementing the consistency tests last week before
the last post was made and, hence, I worked on repository line 1.2
(revision 3303).

I implemented the consistency tests as a new type of run ('ct') similar
to the one for Jw mapping.

The calculations are made for J(0), F_eta and F_R2 separately for each
magnetic field (one at a time). The output results file is similar to
the one for Jw mapping. The user then needs to plot them and look for
consistency with its own criteria (calculation correlation
coefficients,  mean ratios and standard deviations, etc).

Please look at the followinr URL for a listing of the modifications to
old files and also necessary new files.

http://maple.rsvs.ulaval.ca/mediawiki/index.php/Relax_development

The file 'sample_scripts/consistency_tests.py' should be useful to
understand how the new procedure works.

Even if this was done on repository line 1.2, I think it is quite fine
since nothing was deleted but only things added (maybe too much, as I
reproduced the Jw mapping approach, maybe too much as I added lines in
the codes for grace, molmol, etc, maybe too much also since some code is
duplicated from the Jw mapping code). The test-suite still works
perfectly and, so, I think it could be fine to add the tests to the 1.2
line as well... However, if necessary, I could implement the consistency
testing procedure on line 1.3, following your comments as I am quite new
to Python and maybe made things somehow not perfectly...

Please tell me what you think about this.

Cheers,


Sébastien  :)



Edward d'Auvergne wrote:

Hi,

I have previously talked about data set consistency.  For example see
the post at

https://mail.gna.org/public/relax-users/2007-06/msg00001.html

in which a few reasons for inconsistencies have been explained.  I
have, from experience, noticed that small changes in protein
concentration can change the collected relaxation rates significantly
- most likely because of packing interactions.  All samples should
essentially be identical in all respects for the relaxation rates to
be compared.  And the temperate should always be fine tuned between
experiments and spectrometers using methanol (and always checked later
on if there is a large time between collecting the same experiment).

Therefore these tests would be quite useful.  Data consistency is
essential for the model-free results to be correct (as well as reduced
spectral density mapping, SRLS, etc.) as this affects both the
optimisation and model selection and can result in artificial motions
appearing.  However I don't know how these test would currently fit
within relax.  Maybe a new type of analysis should be created for this
(see the pipe.create() user function in the 1.3 line or the
run.create() user function in the 1.2 line).  These ideas should all
go into the 1.3 line (via a branch) as the 1.2 line is stable and no
new major features will be added to this code.  What are the ideas you
have been playing with?

Cheers,

Edward


On 6/15/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:

Hi everyone

During the last months, I was astonished to realize that some spin
relaxation data I had acquired at different fields were not

consistent

between each other. The way I realized that was by seeing discrepancy
between J(0) values calculated with those different datasets.

I looked a little bit in the litterature and found some interesting
consistency tests in a paper by Fushman (Fushman et al., JACS, 1998,
120:10947-10952).

This paper present 2 consistency tests to compare datasets from
different magnetic fields / samples / time / etc.

I think it would be interesting to implement those simple tests in

relax

so the user can, before trying to fit their data, know the quality of
those... Regrettably, very few people look at the consistency of

their

datasets before analysis...

The underlying principle is the same as when looking at

consistency for

J(0). Thus, I think that those two tests and a J(0) test should be
implemented altogether...

I'll try to work a bit on this. Mimicking the code for spectral

density

should be a good starting point.

Am I right ?
Do you see any value in those tests ?

Cheers


Sébastien  :)


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-- 
         ______________________________________
     _______________________________________________
    |                                               |
   || Sebastien Morin                               ||
  ||| Etudiant au PhD en biochimie                  |||
 |||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne                             |||||
 |||| CREFSIP (Universite Laval, Quebec, CANADA)    ||||
  ||| 1-418-656-2131 #4530                          |||
   ||                                               ||
    |_______________________________________________|
         ______________________________________


-- 
         ______________________________________    
     _______________________________________________
    |                                               |
   || Sebastien Morin                               ||
  ||| Etudiant au PhD en biochimie                  |||
 |||| Laboratoire de resonance magnetique nucleaire ||||
||||| Dr Stephane Gagne                             |||||
 |||| CREFSIP (Universite Laval, Quebec, CANADA)    ||||
  ||| 1-418-656-2131 #4530                          |||
   ||                                               ||
    |_______________________________________________|
         ______________________________________

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