Imperial College London

Henry Rzepa

In March, I posted from the ACS meeting in San Diego on the topic of
[Research data: Managing
spectroscopy-NMR](http://www.ch.imperial.ac.uk/rzepa/blog/?p=15916){target="_top"},
and noted a talk by MestreLab Research on how a tool called **Mpublish**
in the forthcoming release of their NMR analysis software **Mestrenova**
could help. With that release [now
out](http://mestrelab.com/software/mnova/download/){target="_top"}, the
opportunity arose to test the system.

I will start by reminding that NMR data associated with a published
article is (or should be) openly free: one should not need a
subscription to the journal to access it (although one might in order to
find it). Now, NMR data as it emerges from a spectrometer is highly
sophisticated, comprising a collection of (sometimes) binary proprietary
files containing the measured free induction decays (FID). Turning this
raw data into an interpretable NMR spectrum, the visual form of the data
that so appeals to human beings, is non trivial. This requires what may
be highly sophisticated software and that in turn means that it may be a
commercial product. Of course there are also examples of non-commercial
open software packages that are best-of-breed; indeed in its early
life-cycle MestreNova was known as MESTREC before becoming a commercial
product. Could one achieve the benefits of both open and fully
functional NMR data with no loss from the original instrument
coupled with the ability to apply top-quality software for its analysis
in an open manner? This is a demonstration of how **Mpublish** achieves
this.

1.  Invoke the URL
    [data.datacite.org/chemical/x-mnpub/10.14469/hpc/1087](http://data.datacite.org/chemical/x-mnpub/10.14469/hpc/1087){target="_top"}
    from a browser
2.  This action queries the metadata deposited with DataCite for the doi
    [10.14469/hpc/1087](http://doi.org/10.14469/hpc/1087){target="_top"}
    and retrieves the first instance of any file associated with that
    dataset that has the format type **chemical/x-mnpub**. You can
    directly view this metadata by invoking just
    [data.datacite.org/10.14469/hpc/1087](http://data.datacite.org/10.14469/hpc/1087){target="_blank"}
    where you can find both mnpub and mnova formats listed. A command
    such as
    [data.datacite.org/chemical/x-mnpub/10.14469/hpc/1087](http://data.datacite.org/chemical/x-mnpub/10.14469/hpc/1087){target="_top"}
    allows the file retrieval to be incorporated into automated
    workflows based just on the doi and the media type desired. Note my
    parenthetical comment above about finding data; here you only need
    its doi to retrieve it!
3.  The URL above downloads a small text file with the suffix **.mnpub**
    which contains in essence two components:
    - A URL pointing directly to an **.mnova** file at the repository
      for which the doi has been issued
    - A signature key derived used to verify that the public key of the
      publisher (the data repository in this instance) was
      counter-signed by Mestrelab.
4.  If you now [download](http://mestrelab.com/){target="_blank"} the
    application program and install it (but for the purpose of this
    demonstration, ignore any requests to try to license the program.
    Use it unlicensed) and open the .**mnpub** file using it, you should
    get the below.The application program has checked the signature key,
    and if valid, proceeds to download a full data file (a **.mnova**
    file in this case), and to analyze and display it within the
    program. The data is fully active; it can be manipulated and
    analysed. Notice in the picture below, the red arrow points to the
    state of the license, in this case not present.  
    ![mn](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2016/08/mn.jpg){.aligncenter
    .size-full .wp-image-16634 decoding="async" width="440"
    srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2016/08/mn.jpg 893w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2016/08/mn-300x191.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2016/08/mn-768x490.jpg 768w"
    sizes="(max-width: 893px) 100vw, 893px"}
5.  It is also possible to apply this procedure to the raw data as it
    emerges from the (Bruker) spectrometer, and compressed into a .zip
    archive. The MestreNova software will automatically process the
    contents by applying various default parameters, although the result
    may not correspond exactly to that present in *e.g.* the equivalent
    .mnova file (which may have had specific parameters applied).

It is my hope that anyone who records NMR data and processes it using
software such as MestreNova will now consider using the mechanism above
to accompany their submitted articles, rather than just automatically
pasting a static image of the spectrum into a PDF file as \"supporting
information\". This is part of what is meant by \"managed research
data\" (RDM).

One cannot help but note that many types of scientific instrument
nowadays come with bespoke software for analysing the data they produce.
Very often this software is unavailable to anyone who has not purchased
the instrument itself. To make the data available to others, the
processed data and its visual interpretation often have to be reduced,
with much consequent information loss, to a lowest common
denominator format such as Acrobat/PDF. Here we see a mechanism for
avoiding any such information loss whilst enabling, for that dataset
only, the full potential for (re)analysing the data. It will be
interesting to see if other examples of this model or its equivalent
emerge in the near future.

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[https://orcid.org/0000-0002-8635-8390](https://orcid.org/0000-0002-8635-8390){target="_blank"
rel="author"}
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In March, I posted from the ACS meeting in San Diego on the topic of Research data: Managing spectroscopy-NMR, and noted a talk by MestreLab Research on how a tool called
<strong>
 Mpublish
</strong>
in the forthcoming release of their NMR analysis software
<strong>
 Mestrenova
</strong>
could help. With that release now out, the opportunity arose to test the system.

Messaggi di Rogue Scholar

Managing (open) NMR data: a working example using Mpublish.