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Hi everyone,
<div class="">NeXus was originally both a standard for defining how data should be organized in files and a unified API for reading and writing those files, irrespective of the physical file format, HDF4, HDF5, or XML. Thanks mainly to the work that Mark Koennecke
put into the C-API, it achieved both goals seamlessly. I think it was a remarkable technical achievement. To some extent, the two components were independent of each other, but not entirely. For example, HDF4 did not allow group attributes, so for a long time,
they were not part of the definitions. Now that HDF4 is obsolete, the NeXus definitions have evolved to use more and more of the features that HDF5 provides, many of which have become an essential part of the standard. </div>
<div class=""><br class="">
</div>
<div class="">I think there are therefore two questions that need to be clarified, preferably before we next meet. The first is whether the proposed alternative physical file formats will allow the same type of hierarchical data organization and features that
have now become part of the standard. If they didn’t, this would probably be a deal-breaker, unless there is a way of interfacing, say, regular HDF5 NeXus files to the new file formats, in much the same way that HDF5 handles external links. </div>
<div class=""><br class="">
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<div class="">The second is whether there is a need to revive the API to handle the new formats, so that we are not faced with the situation that Tobias warned about with a large fraction of the user community unable to read such files. The reason the API became
deprecated is, in my view, that we have depended too much on one or two people (i.e., Mark in the case of the C-API) to take all the responsibility for maintaining it, so that supporting new HDF5 features, such as virtual data sets or even variable-length-strings,
fell entirely on them. While an increasing number of facilities have become dependent on NeXus, very few of them, if any, have committed resources to maintaining it, so it has become an activity that many of us squeeze in when we have free time from our other
responsibilities. If facilities like Alba, and presumably others, feel that they are being held back by technical limitations of HDF5, then it might be necessary to rethink the NeXus support model, so that API development is revived by being integrated into
other facility software development projects, such as Mantid or Dials. It would probably save the facilities money in the long term, but it would require NeXus to be less of a part-time activity. Or we need to encourage more people to contribute, in the way
the more successful open-source projects are run. I would certainly welcome additional support for the Python API for the same reasons.</div>
<div class=""><br class="">
</div>
<div class="">With best regards,</div>
<div class="">Ray</div>
<div class="">
<div class="">
<div class="">-- <br class="">
Ray Osborn, Senior Scientist<br class="">
Materials Science Division<br class="">
Argonne National Laboratory<br class="">
Argonne, IL 60439, USA<br class="">
Phone: +1 (630) 252-9011<br class="">
<a href="mailto:ROsborn@anl.gov" class="">Email: ROsborn@anl.gov</a><br class="">
<br class="">
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Apr 7, 2022, at 12:16 PM, Watts Benjamin (PSI) via NeXus <<a href="mailto:nexus@shadow.nd.rl.ac.uk" class="">nexus@shadow.nd.rl.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi Tobias,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""> I agree that we have spent the past decade recommending HDF5, but at the same time we have been saying that NeXus is about the organisation of data within the container, not the container file format
itself. I can see that you feel surprised by the sudden discussion of other file formats, just as I was surprised to hear the community talking about it at the recent NFDI workshop. I am only advocating for discussion and I would like to hear your input.<span class="Apple-converted-space"> </span><span class="">I
agree that multiple backends will introduce higher support requirements that NeXus doesn't currently have resources for.</span><span class="Apple-converted-space"> </span>Your preference for NeXus referring to a (small) defined set of file formats is a valid
view point and I agree that there are practicalities to consider. I view the next telco as just the restart of an old discussion and nothing can really change until a proposal is brought to a NIAC meeting (and accepted).</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Cheers,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Ben<br class="">
</div>
</div>
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Tobias Richter <<a href="mailto:Tobias.Richter@ess.eu" class="">Tobias.Richter@ess.eu</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, 7 April 2022 6:23:43 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Discussion forum for the NeXus data format;
<a href="mailto:nexus@nexusformat.org" class="">nexus@nexusformat.org</a><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Watts Benjamin (PSI); Alexander Debus; Nicolas Soler; Franz Pöschel; Emilio Centeno Ortiz<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Nexus] HDF5 as NeXus file format</font>
<div class=""> </div>
</div>
<div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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<span class="">Hi all,<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class="">According to this discussion from a decade ago HDF5 is singled out as the only preferred physical file format:<span class="Apple-converted-space"> </span><a href="https://www.nexusformat.org/NIAC2012" style="color: blue; text-decoration: underline;" class="">https://www.nexusformat.org/NIAC2012</a><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<ul type="disc" style="margin-bottom: 0cm;" class="">
<li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(81, 81, 81); background-color: white; background-position: initial initial; background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family: "PT Sans", sans-serif;" class="">NeXus guiding statements:<o:p class=""></o:p></span>
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<li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(81, 81, 81); background-color: white; background-position: initial initial; background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family: "PT Sans", sans-serif;" class="">The main focus of the NeXus community is to further develop the dictionaries, base classes and application definitions.<o:p class=""></o:p></span></li><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(81, 81, 81); background-color: white; background-position: initial initial; background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family: "PT Sans", sans-serif;" class="">The NIAC is a forum for resolving issues.<o:p class=""></o:p></span></li><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(81, 81, 81); background-color: white; background-position: initial initial; background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family: "PT Sans", sans-serif;" class="">The NIAC acts as a custodian for NeXus: definitions, examples, documentation, reference implementations.<o:p class=""></o:p></span></li><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(81, 81, 81); background-color: white; background-position: initial initial; background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family: "PT Sans", sans-serif;" class="">NeXus can be mapped to different physical file formats:<o:p class=""></o:p></span>
<ul type="square" style="margin-bottom: 0cm;" class="">
<li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(81, 81, 81); background-color: white; background-position: initial initial; background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family: "PT Sans", sans-serif;" class="">HDF5 is the preferred physical file format.<o:p class=""></o:p></span></li><li class="MsoNormal" style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(81, 81, 81); background-color: white; background-position: initial initial; background-repeat: initial initial;">
<span style="font-size: 13.5pt; font-family: "PT Sans", sans-serif;" class="">NeXus-XML is the currently supported ASCII file format.<o:p class=""></o:p></span></li></ul>
</li></ul>
</li></ul>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class="">Technically you can map into different backends. Yes. XML is still sort of supported. At the time it was requested that other options would get the official blessing (YAML being specifically asked for) but for practical exchange between facilities
the consensus was to stick with HDF5.<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class="">There no longer is a recommended or fully maintained abstraction layer (like NAPI) to do an on the fly translation between backends. Who would be in charge of defining how the “official” mapping into sqlite or whatever would look like? How many
backends can the community commit to support in the long run?<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class="">When tools that are currently developed/supported/maintained to “read” NeXus/HDF5 fail to work with what gets handed out, we are in a worse situation than we are now. Note: What facilities do internally for performance optimisations or other
reasons could be different, if it stays internal. But I am clearly a lot less open minded about producing non-HDF5 files with a “NeXus” label than Ben. Maybe I missed some decisions that were taken lately in this direction or we’re no longer interested in
being able to read each other’s files. Should either be the case, I’ll be quiet.<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class="">Best wishes,<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class="">Tobias<o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span class=""><o:p class=""> </o:p></span></div>
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<b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">NeXus <<a href="mailto:nexus-bounces@shadow.nd.rl.ac.uk" class="">nexus-bounces@shadow.nd.rl.ac.uk</a>> on
behalf of "Watts Benjamin (PSI) via NeXus" <<a href="mailto:nexus@shadow.nd.rl.ac.uk" class="">nexus@shadow.nd.rl.ac.uk</a>><br class="">
<b class="">Reply to:<span class="Apple-converted-space"> </span></b>Discussion forum for the NeXus data format <<a href="mailto:nexus@shadow.nd.rl.ac.uk" class="">nexus@shadow.nd.rl.ac.uk</a>><br class="">
<b class="">Date:<span class="Apple-converted-space"> </span></b>Thursday, 7 April 2022 at 17:10<br class="">
<b class="">To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:nexus@nexusformat.org" class="">nexus@nexusformat.org</a>" <<a href="mailto:nexus@nexusformat.org" class="">nexus@nexusformat.org</a>><br class="">
<b class="">Cc:<span class="Apple-converted-space"> </span></b>Benjamin Watts <<a href="mailto:benjamin.watts@psi.ch" class="">benjamin.watts@psi.ch</a>>, Alexander Debus <<a href="mailto:a.debus@hzdr.de" class="">a.debus@hzdr.de</a>>, Nicolas Soler <<a href="mailto:nsoler@cells.es" class="">nsoler@cells.es</a>>,
Franz Pöschel <<a href="mailto:f.poeschel@hzdr.de" class="">f.poeschel@hzdr.de</a>>, Emilio Centeno Ortiz <<a href="mailto:ecenteno@cells.es" class="">ecenteno@cells.es</a>><br class="">
<b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: [Nexus] HDF5 as NeXus file format<o:p class=""></o:p></span></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
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<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class="">Hi Gabriel,<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class=""> NeXus is officially not dependent on HDF5 and we are definitely open minded about implementing the NeXus<span class="Apple-converted-space"> </span><i class="">data
format</i><span class="Apple-converted-space"> </span>on<span class="Apple-converted-space"> </span><i class="">file formats</i><span class="Apple-converted-space"> </span>other than HDF5. We plan to discuss such issues at our<span class="Apple-converted-space"> </span><a href="https://www.nexusformat.org/Telco_20220426.html" style="color: blue; text-decoration: underline;" class="">next
teleconference</a><span class="Apple-converted-space"> </span>on April 26th and I invite you to join us. Are there specific container file formats that you are interested in?<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class="">Cheers,<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class="">Ben<o:p class=""></o:p></span></div>
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<span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></p>
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<div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="" class="">From:</span></b><span style="" class=""><span class="Apple-converted-space"> </span>NeXus <<a href="mailto:nexus-bounces@shadow.nd.rl.ac.uk" class="">nexus-bounces@shadow.nd.rl.ac.uk</a>> on behalf of Gabriel Jover Manas
via NeXus <<a href="mailto:nexus@shadow.nd.rl.ac.uk" class="">nexus@shadow.nd.rl.ac.uk</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, 7 April 2022 4:47 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:nexus@nexusformat.org" class="">nexus@nexusformat.org</a><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Gabriel Jover Manas; Nicolas Soler; Emilio Centeno Ortiz<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>[Nexus] HDF5 as NeXus file format</span><span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div>
<div class="">
<div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 12pt;" class=""> <o:p class=""></o:p></span></div>
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<div class="">
<div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 12pt;" class="">Dear NeXus Users Community,<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class="">Last NFDI NeXus Workshop was a great opportunity to meet the community and learn from the experience of other scientists and institutions.<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class="">Here at ALBA we are working on the integration of NeXus files in our data analysis workflows.<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class="">In this scope we are interested on investigating alternatives to hdf5 as NeXus file format, in terms of slice read/write performance, read-write-many
capabilities and convenient reading.<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class="">Would the community be open to decoupling the data format (NeXus) from the file format (HDF5)?<br class="">
Is there already any effort in the community in this direction?<br class="">
Is anyone else also interested?<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class="">Best regards,<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class="">Gabriel<o:p class=""></o:p></span></div>
<div style="margin-top: 0px; margin-bottom: 0px; margin-left: 36pt;" class=""><span style="font-size: 12pt;" class=""><o:p class=""> </o:p></span></div>
<div class="">
<div style="margin: 0cm 0cm 0cm 36pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 12pt;" class="">--<o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 9pt; color: rgb(17, 46, 80);" class=""><a href="http://www.albasynchrotron.es/" target="_blank" style="color: blue; text-decoration: underline;" class="">www.albasynchrotron.es</a></span></b><b class=""><span style="font-size: 7.5pt; color: rgb(17, 46, 80);" class=""><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span></span></b><b class=""><span style="font-size: 9pt; color: rgb(17, 46, 80);" class=""><a href="mailto:Gabriel.Jover@cells.es" style="color: blue; text-decoration: underline;" class="">Gabriel.Jover@cells.es<span class="Apple-converted-space"> </span></a>|<span class="Apple-converted-space"> </span><a href="https://www.albasynchrotron.es/en/about/legal-notice" target="_blank" style="color: blue; text-decoration: underline;" class="">legal
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<b class=""><span style="font-size: 8pt; color: rgb(138, 138, 138);" class="">Please, do not print this e-mail unless it is absolutely necessary.<span class="Apple-converted-space"> </span><br class="">
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Si ha recibido este correo por error, le informo de que puede contener información confidencial y privada y que está prohibido su uso. Le agradeceré que lo comunique a su remitente y lo elimine. Gracias.<br class="">
If you have received this e-mail in error, please note that it may contain confidential and private information, therefore, the use of this information is strictly forbidden. Please inform the sender of the error and delete the information received. Thank you.</span><o:p class=""></o:p></div>
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">NeXus
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""><a href="mailto:NeXus@nexusformat.org" class="">NeXus@nexusformat.org</a></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""><a href="https://lists.nexusformat.org/mailman/listinfo/nexus" class="">https://lists.nexusformat.org/mailman/listinfo/nexus</a></span></div>
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