Hi Edward,
let me try to clarify, as far as I understand.
The original code of the Maple extension was written in Maple and
probably directly put into Matlab in 2000-2001 by Martin and Nikolai.
They did relaxation dispersion fitting back then, and this was done in
Matlab
(You can find a statement about this fitting in Matlab in Tollinger, M.;
Skrynnikov, N.; Mulder, F.; Forman-Kay, J.; Kay, L. J Am Chem Soc 2001,
123, 11341–11352.)
Martin has been very active ever since then in the field of CPMG
relaxation dispersions, so he certainly used the Matlab functions from
those days on (probably until now). So I am not surprised that there
might have been a modification or extension in some of the files, such
that some files has a date of creation in 2005.
To resolve that issue, you might probably just extend Martin's copyright
period.
I got the code from Martin in 2010 (as Matlab code), I believe, in the
context of a number of joint publications
(Schanda, P.; Brutscher, B.; Konrat, R.; Tollinger, M. J Mol Biol 2008,
380, 726–741.
Bruschweiler, S.; Schanda, P.; Kloiber, K.; Brutscher, B.; Kontaxis, G.;
Konrat, R.; Tollinger, M. J Am Chem Soc 2009, 131, 3063–3068.
Tollinger, M.; Sivertsen, A. C.; Meier, B. H.; Ernst, M.; Schanda, P. J
Am Chem Soc 2012, 134, 14800–14807.)
As I did not have Matlab in 2010, I started shuffling some of the code
into octave, and then later into python.
In 2013, Mathilde, Dominique and I then wrote proper functions in
python, which are the ones that we contributed to relax. There are a
number of functions, which you all included, that either work with
Bloch-McConnell matrices in complex or real formulation, or with the
Nikolai/Maple-derived function.
The sim_all.m files that I have attached previously are mostly from
Martin, and I did some minor changes to them.
So, I guess that this would be a way of fixing the date issue properly:
2000-2001 - as Maple code developed by Nikolai Skrynnikov and fixes by
Martin Tollinger.
2000-2005 - extension of Matlab code by Martin Tollinger
2010-2013 - Python code by Paul Schanda
2013 - Python code by Mathilde Lescanne and Dominique Marion
I cannot tell you the origin of each line of code (and I doubt that
anybody of the mentioned persons could), but this is basically the
history of the code.
I hope that resolves this issue.
paul
On 30.07.13 19:58, Edward d'Auvergne wrote:
Hi Paul,
I have managed to re-piece the history of the code in the file
lib/dispersion/ns_2site_expanded.py as follows:
2000-2001 - as Maple code developed by Nikolai Skrynnikov and fixes by
Martin Tollinger.
2010-2013 - as Matlab code that you translated and extended.
2013 - as Python code translated from the Matlab code by Mathilde
Lescanne and Dominique Marion, and again extended.
I have a feeling that I don't have this history correct or complete
yet. This code also appears in the funNikolai.m file inside the
sim_all.tar file (https://gna.org/support/download.php?file_id=18404)
attached to https://gna.org/task/?7712#comment5. However this file
has the date 2005.
Therefore there appears to have been a Maple to Matlab code conversion
between 2001 and 2005, unless I am mistaken. Do you know why there
are Matlab files with the 2005 date, and what their origin is?
Cheers,
Edward
--
Paul Schanda, Ph.D.
Biomolecular NMR group
Institut de Biologie Structurale Jean-Pierre Ebel (IBS)
41, rue Jules Horowitz
F-38027 Grenoble
France
+33 438 78 95 55
paul.schanda@xxxxxx
http://www.ibs.fr/groups/biomolecular-nmr-spectroscopy?lang=en
Re: Missing code history of the 'NS 2-site expanded' model.