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<p>Hi Everyone,</p>
<p> My understanding is that the core NeXus mission has only concerned the organisation of the data. The container file format was only within our scope for the practical reasons of demonstrating how to implement the NeXus structures. We recommended HDF5
because we did not see viable alternatives for a long time. <br>
</p>
<p><br>
</p>
<p>I think that there are both practical and ideological aspects to the discussion about file formats for NeXus and it is a bit confronting for some of us because we see conflict between these aspects. On the one hand, we should encourage people using file
formats other than HDF5 and XML to organise their data using NeXus. On the other hand, we don't want to encourage a "wild west" in file formats where reading archived files becomes a hunt for obscure libraries. On this point - what is the role that NeXus should
play? Certainly, NeXus should only promote file formats that are capable of expressing the NeXus hierarchies. NeXus should also document how the data hierarchies are expressed in each file format (I think we can do this in a more formal way than we currently
do). If NeXus is to do any discrimination between file formates, I would like for us to come up with a set of criteria for file formats to meet in order to gain NeXus approval. NeXus does not currently have the resources to support further file formats in
the NeXus libraries (NAPI) and perhaps community support could be one of the criteria for approval.<br>
</p>
<p><br>
</p>
<p>Cheers,</p>
<p>Ben<br>
</p>
<p><br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Osborn, Raymond <rosborn@anl.gov><br>
<b>Sent:</b> Thursday, 7 April 2022 9:42:50 PM<br>
<b>To:</b> Discussion forum for the NeXus data format<br>
<b>Cc:</b> Tobias Richter; nexus@nexusformat.org; Watts Benjamin (PSI); Alexander Debus; Nicolas Soler; Franz Pöschel; Emilio Centeno Ortiz<br>
<b>Subject:</b> Re: [Nexus] HDF5 as NeXus file format</font>
<div> </div>
</div>
<div>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="">
</div>
<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="">
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<div class="" style="margin-top:0px; margin-bottom:0px">Hi Tobias,</div>
<div class="" style="margin-top:0px; margin-bottom:0px"> 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>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Cheers,</div>
<div class="" style="margin-top:0px; margin-bottom:0px">Ben<br class="">
</div>
</div>
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<font class="" style="font-size:11pt" face="Calibri, sans-serif"><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>
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<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class="">Hi all,</span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class=""> </span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<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" class="" style="color:blue; text-decoration:underline">https://www.nexusformat.org/NIAC2012</a></span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class=""> </span></div>
<ul class="" style="margin-bottom:0cm" type="disc">
<li class="MsoNormal" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif; color:rgb(81,81,81); background-color:white">
<span class="" style="font-size:13.5pt; font-family:"PT Sans",sans-serif">NeXus guiding statements:</span>
<ul class="" style="margin-bottom:0cm" type="circle">
<li class="MsoNormal" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif; color:rgb(81,81,81); background-color:white">
<span class="" style="font-size:13.5pt; font-family:"PT Sans",sans-serif">The main focus of the NeXus community is to further develop the dictionaries, base classes and application definitions.</span></li><li class="MsoNormal" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif; color:rgb(81,81,81); background-color:white">
<span class="" style="font-size:13.5pt; font-family:"PT Sans",sans-serif">The NIAC is a forum for resolving issues.</span></li><li class="MsoNormal" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif; color:rgb(81,81,81); background-color:white">
<span class="" style="font-size:13.5pt; font-family:"PT Sans",sans-serif">The NIAC acts as a custodian for NeXus: definitions, examples, documentation, reference implementations.</span></li><li class="MsoNormal" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif; color:rgb(81,81,81); background-color:white">
<span class="" style="font-size:13.5pt; font-family:"PT Sans",sans-serif">NeXus can be mapped to different physical file formats:</span>
<ul class="" style="margin-bottom:0cm" type="square">
<li class="MsoNormal" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif; color:rgb(81,81,81); background-color:white">
<span class="" style="font-size:13.5pt; font-family:"PT Sans",sans-serif">HDF5 is the preferred physical file format.</span></li><li class="MsoNormal" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif; color:rgb(81,81,81); background-color:white">
<span class="" style="font-size:13.5pt; font-family:"PT Sans",sans-serif">NeXus-XML is the currently supported ASCII file format.</span></li></ul>
</li></ul>
</li></ul>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class=""> </span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<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.</span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class=""> </span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<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?</span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class=""> </span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<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.</span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class=""> </span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class="">Best wishes,</span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class="">Tobias</span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class=""> </span></div>
<div class="" style="margin:0cm; font-size:11pt; font-family:Calibri,sans-serif">
<span class=""> </span></div>
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<div class="" style="margin:0cm 0cm 0cm 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<b class=""><span class="" style="font-size:12pt">From:<span class="Apple-converted-space"> </span></span></b><span class="" style="font-size:12pt">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</span></div>
</div>
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<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt">Hi Gabriel,</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt"> 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" class="" style="color:blue; text-decoration:underline">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?</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt">Cheers,</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt">Ben</span></div>
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<span class="" style="font-size:12pt"> </span></p>
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<hr class="" width="100%" size="0" align="center">
</span></div>
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<div class="" style="margin:0cm 0cm 0cm 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<b class=""><span class="" style="">From:</span></b><span class="" style=""><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 class="" style="font-size:12pt"></span></div>
<div class="">
<div class="" style="margin:0cm 0cm 0cm 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt"> </span></div>
</div>
</div>
<div class="">
<div class="" style="margin:0cm 0cm 0cm 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt">Dear NeXus Users Community,</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt">Last NFDI NeXus Workshop was a great opportunity to meet the community and learn from the experience of other scientists and institutions.</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt">Here at ALBA we are working on the integration of NeXus files in our data analysis workflows.</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt">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.</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt">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?</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt"> </span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt">Best regards,</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt">Gabriel</span></div>
<div class="" style="margin-top:0px; margin-bottom:0px; margin-left:36pt"><span class="" style="font-size:12pt"> </span></div>
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<span class="" style="font-size:12pt">--</span></div>
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<div class="" style="margin-top:0px; margin-bottom:0px"><a href="http://www.albasynchrotron.es/" target="_blank" class="" style="color:blue; text-decoration:underline"><span class="" style="color:windowtext; text-decoration:none"><span class="" style="color:blue; border:1pt solid windowtext; padding:0cm"><img id="_x0000_i1025" alt="Image removed by sender. ALBA Synchrotron" class="" style="width:1.2291in; height:0.5729in" width="118" height="55" border="0" src="cid:~WRD0000.jpg"></span></span></a></div>
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<b class=""><span class="" style="font-size:12pt; font-family:Arial,sans-serif; color:rgb(17,46,80)">Gabriel Jover-Mañas</span></b></div>
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<span class="" style="font-size:9pt; font-family:Arial,sans-serif">Scientific Data Management<br class="">
Computing Division<span class="Apple-converted-space"> </span></span></div>
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<b class=""><span class="" style="font-size:10pt; font-family:Arial,sans-serif">ALBA SYNCHROTRON LIGHT SOURCE</span></b></div>
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<span class="" style="font-size:9pt; font-family:Arial,sans-serif"><a href="http://www.albasynchrotron.es/en/about/coming-to-alba" target="_blank" class="" style="color:blue; text-decoration:underline">Carrer de la Llum 2-26 | 08290 | Cerdanyola del Vallès|
Barcelona | Spain<span class="Apple-converted-space"> </span></a><br class="">
(+34) 93 592 4471<span class="Apple-converted-space"> </span></span></div>
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<b class=""><span class="" style="font-size:9pt; color:rgb(17,46,80)"><a href="http://www.albasynchrotron.es/" target="_blank" class="" style="color:blue; text-decoration:underline">www.albasynchrotron.es</a></span></b><b class=""><span class="" style="font-size:7.5pt; color:rgb(17,46,80)"><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span></span></b><b class=""><span class="" style="font-size:9pt; color:rgb(17,46,80)"><a href="mailto:Gabriel.Jover@cells.es" class="" style="color:blue; text-decoration:underline">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" class="" style="color:blue; text-decoration:underline">legal
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<b class=""><span class="" style="font-size:8pt; color:rgb(138,138,138)">Please, do not print this e-mail unless it is absolutely necessary.<span class="Apple-converted-space"> </span><br class="">
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Gràcies.<br class="">
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></div>
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<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">NeXus
mailing list</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important"><a href="mailto:NeXus@nexusformat.org" class="">NeXus@nexusformat.org</a></span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important"><a href="https://lists.nexusformat.org/mailman/listinfo/nexus" class="">https://lists.nexusformat.org/mailman/listinfo/nexus</a></span></div>
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