Talk:NMR Software

Types of software to list
I think that it could also be interesting to separate things

software for analysis of the spectra

biomolecular NMR * structure determination * analysis of the structure * dynamic analysis * chemical shift this could also be quite interesting http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_e.py * bioanalysis software, secondary structure prediction ...

bio informatics software should also have so dedicate place I think, software like profunc to determine the function of protein using it's structure, could be interesting. Otherwise their is also all tools based on structure to enhance sequences alignements.

chemical NMR * database software * software to find the right topology of the molecule * QM calculation

solide state NMR * Experiment simulation software * May be their exists something arround the PISEMA experiment that allow to fit the helix on the spectra.

online software - that you've mentioned is another category. we also have Online data tools page Evgeny Fadeev 14:13, 25 April 2008 (MDT)

unix & other os stuff
add Unix and other OS tricks? Looks like important part of life... A lot of that is already online - so we could just collect good links. Evgeny Fadeev 21:26, 24 April 2008 (MDT)

Website scope
We face their a problem that looks like the problems we have defining what is the of partial charges on atoms, when we are doing quantum mechanics calculation. Unfortunately their is no operator, that define partial charge on a atom, here it's the same. Where should we stop. On unix tricks I think that I'll have too much things to add, add generally unix tricks are more on manipulating data in a general context than manipulating them in a specialized context.

On some point of view it belong also to NMR, after it depends on what you want to do with this blog.

The little articles I wrote where not really precise, and didn't get really depth in the subject, and where more theoretical than the experimental point of view. But nowadays, good articles on NMR, are for instance the one about SAIL, or also the one from pnas, that show how much information is contained in chemical shift, so enhancement on one side of the sensibility and the throughput of the NMR spectrometer : - through 1 mm coils ( could allow using lower amount of the expensive SAIL aminoacide ) ( 72 µg of 10 kDa protein where needed to determine the structure, the experiment last twice as long as normally ) - reduced dimensionality experiments ( probably even more interesting with SAIL amino acids ) - may be DNP - multi coil NMR probs ( up to 8 where already done, but why not more ? )

and maybe : encapsuled proteins

And on the other hand : - Using the chemical shift for structure determination ( or/and refinement ) - Paramagnetic probes - Fast experiments, Fast HQSC

On MRI the natural contrast agent : hyperpolarized water. Seems to me something conceptually very interesting : adding signal instead of making it dacay faster

Seems to me the most important point &rarr; About Unix there is a lot of stuff online - maybe we can just point to them. Nobody has time to write quality stuff about everything. But covering some Bioinformatics and computation biology topics is a good idea.

Maybe there is no need to artificially try to stretch scope - just write about what is relevant. If you want to write about some bioinformatics package - go ahead. That is nobody will be objecting to to that but there is no reason to push that way. The primary goal of this is to create a quality compilation of MR software. Evgeny Fadeev 13:51, 25 April 2008 (MDT)

page name
Looks like this question applies to many other pages as well.

It's quite natural that as more stuff is added, purpose of the page changes.

Should we rename this page to just "Software"? Evgeny Fadeev 13:36, 25 April 2008 (MDT)

So I guess when we add link or page to some non-MR software we'll change name of document to just "Software"? Evgeny Fadeev 13:46, 25 April 2008 (MDT)

Classification of software by main functions
=> It's possible to do pages that are generated automatically, so that if we change the name of the software it will change name, a software could be in different subsections, for instance a software that belong to class B, and class C:A, will appear automatically on 4 pages : all softwares, B softwares, all C software, A software

=>Unfortunately automatic title generation will make wiki software more complex and there will be side-effects. Each time page name is changed - wiki creates a redirection page so that links won't break... you can imaging redirect chains- not that good.

What you are suggesting for software classing could be done with a special extension that could also work for version tracking in manuals: iNMR SpinWorks Sparky NMRPipe There will also have to be another extension that creates selecting header on top. I've already promised on AMMRL meeting that I'll do that by May.

This basically looks like tagging. Evgeny Fadeev 12:06, 25 April 2008 (MDT)

By OS platform
There is another type of classification: os platform. Evgeny Fadeev 13:46, 25 April 2008 (MDT)

By features
This is most fine-grained - probably in form of table some functional categories. E.g. in processing packages: what formats are understood, can user manipulate data directly, etc.

Creating these comparisons won't be quick but very gradual because one person can know it all.

By type of license
shareware, open source, commerical