Network for Advanced NMR - User contributions [en]

Onboarding Guide

2026-06-02T19:55:58Z

Qcheng: Added the link to the manage facility users page

== Overview of Onboarding Steps ==

* Facility added administratively
* A facility manager/director is linked to the facility
* Facility information populated
* Spectrometers and Probes are added and linked together
* NAN users are added to the facility and NDTS settings managed on a per-user basis
* Gateway identified, installed, and configured
* NDTS installed and configured on spectrometers
* Manage operations

== Populating facility, spectrometer, and probe information ==
The information populated for the ''facility, spectrometer, and probe pages'' will appear on the NAN web-portal facility page as well as metadata linked to harvested datasets.

'''''NOTE: All information is fully editable at any time so do not fret over getting information perfect initially.'''''

'''STEPS''':
# A NAN administrator (markm@uchc.edu) will create the facility on the NAN web portal. Information that is needed includes the following, but don't fret it all can be edited later:
#* Long name of the facility (e.g. National Magnetic Resonance Facility at Madison)
#* Short name of the facility (e.g. NMRFAM). Note that the short name and institution will appear as the facility for datasets and shown as a column in the data browser. (e.g. NMRFAM - UW-Madison)
#* Primary facility website URL (e.g. https://nmrfam.wisc.edu)
#* Facility manager or director - who must have an NMRhub account
# Once created the facility manager or director that was added to the facility will have access to populate additional information on the NAN portal.
#* See the [[Facility Dashboards]] wiki page for full details on editing facility information
#* They should see a box in the lower left-hand corner indicating the NMR facility they are acting on behalf.
#** Most users will see a single facility, but if a user were associated with more than one facility they would be able to choose the facility they are acting on from the list.
#* They should also see the Facility Dashboards menu item appear on the Navigation bar.
# Finish entering the facility information. Full instructions may be found on the [[Facility Information]] wiki page, but briefly:
#* Add a facility description
#* Add services that the facility provides and updating the service blurb from the default if desired
#* Add additional website URLs if desired (e.g. adding a URL to rates)
#* Add addresses
#* Add additional staff and choose their '''roles''', '''responsibilities''', and '''expertise'''
#** '''''NOTE: All users added have edit access to the facility and instruments and also the ability to see all data harvested from the facility'''''
#** '''''NOTE: While a users contact information may be typed in manually, the best approach is to use the "Link an NMRhub user" at the top of the box when adding a new user. We recommend only entering information manually if the user will never have a NMRhub (NMRbox/NAN). We also recommend users update their NMRhub profile if information is out-of-date.'''''
#* Add primary contacts using the pull-down list of already entered staff
# Save the facility information
#* '''''NOTE: We recommend using the SAVE button throughout the process so as to not lose data'''''
# Add spectrometers (see the [[Spectrometers|Managing Spectrometers]] wiki page for full instructions - including how NAN defines a spectrometer)
#* Click add Spectrometer and fill out the form. Note that the name should be descriptive, but yet reasonably short as it will appear as a column in the dataset browser
# Add probes (see the [[Probes]] wiki page for full instructions)
#* Click Add probe and fill out the form.
#* Note that the probe name is automatically built based on the information provided including the size, model, and nuclei/channel information, as well as the gradients. Thus, it is best to keep the probe Model to a short value (e.g. TXO, TCI). Keep information such as the field strength, the length, serial number, nuclei, etc. out of the Model as it will be redundant in the probe name.
# Use the manage instruments page to link a probe to a spectrometer and add an install date.
#* Note: the install date is used to calculate which probe is installed in a spectrometer at any given time and thus which probe is associated with datasets collected in the time frame. Thus, it is critical that an install state date is added and that the installed probe is changed on the NAN portal when probes are changed. If you forget to change the probe install date it can be done retroactively.

== [[Manage Facility Users|Managing Facility Users]] ==
Facility managers must add a list of NAN users to their facilities. This is critical for a few reasons:

* it controls the list of NAN users that appears on the NDTS GUI (rather than the users needing to search a never-endling list of all NAN users)
* it controls the list of users that a facility manager may reassign data to
* it allows NDTS settings to be defined on a per user basis
* it allows mapping of NAN users to local spectrometer workstation accounts or allows the local workstation account to be mapped to nobody

'''''NOTE: There is a "Any unspecified" user that appears in the Manage Facility Users page. It is important that the NDTS settings be defined for this user. If the local workstation user is not defined in the Manage Facility Users page then NDTS will use the NDTS settings for the "Any unspecified" user to dictate whether data should be harvested in who it should be assigned to, if anyone. Note that if the datasets are not assigned to a NAN user then only facility staff will have access to them and they may reassign the data to the proper person from the data browser.'''''

'''''NOTE: Users may be added individually, but we also allow all the users with an email domain to be added automatically which can make adding users much easier for a facility.'''''

== NDTS Installation and Configuration ==
Identify a computer that will be used as the Gateway. See the Joining NAN page for technical details. Ideally this is a dedicated computer.

Main Page

2025-07-21T17:50:39Z

Qcheng: spelling correction: byond -> beyond

{{DISPLAYTITLE:User Documentation for the Network of Advanced NMR (NAN)}}
{{search}}
__NOTOC__
<div class="nan-box" style="border: 2px solid #444; background: #F5FAFF; padding: 10px; margin-bottom: 15px;">
<h2 class="nan-title" style="background: #CEDFF2; color: black; padding: 10px; margin: 0;">What is NAN?</h2>
[https://usnan.org NAN] is a collaborative initiative to develop and operate a shared distributed resource for nuclear magnetic resonance (NMR) with the goal of democratizing NMR, making it more accessible and efficient for applications in biology, chemistry, materials science and other fields, and to foster good data stewardship practices. NAN was established by an NSF midscale (RI2) grant to [https://health.uconn.edu/ UConn Health], [https://www.uga.edu/ UGA], and [https://www.wisc.edu/ UW-Madison]. NAN offers open-access to two 1.1 GHz NMR instruments specialized for solids (UW-Madison) and solutions (UGA), along with a roster of additional NMR instruments at participating facilities which may be discovered through the web portal. Beginning in July 2025, membership in NAN is widened to encompass additional NMR facilities beyond the initial three facilities.

NAN provides a suite of '''[[Knowledgebases]] (KBs)''' in Bio Solids, Material Solids, Bio Solutions, and Metabolomics that comprehensively guide novice and expert users through discovering how NMR may be utilized to study interesting scientific problems as well as KB datasets with all the resources needed to recapitulate those experiments. NAN member nodes help to contribute additional KB content and new KB datasets.

Portal dashboards provide tools for (1) facility staff to manage facility, instrument, and probe information, as well as manage facility users, (2) PIs to create projects and manage lab members, and (3) a virtual Network Operations Center (vNOC) for monitoring NAN.

A distinguishing feature of NAN is the '''[[NAN Data Transport System|NAN Data Transport System (NDTS)]]''' [[NAN Data Transport System|a]]<nowiki/>nd [[Data Browser|'''Data Browsers''']]. NDTS automatically harvests experimental data and archives it in a secure repository. Datasets are linked with rich metadata such as instrument, parameters, user, project, sample, and other information. Users view and manipulate data in an advanced Data Browser where they can edit experiments, add notes, classify experiments, and organize data into projects, studies, and collections. PIs are stewards of data collected in their lab and control access. Users can create detailed sample records and link samples with datasets.

For a full breakdown of capabilities across the portal, see the '''[[Feature Summary]].'''

'''Interested in having your NMR facility join as a NAN node? Checkout the [[Joining NAN|Joining NAN page]] for more information.'''
</div>

<div class="nan-box" style="border: 2px solid #444; background: #EEF5E8; padding: 10px; margin-bottom: 15px;">
<h2 class="nan-title" style="background: #B3D1A7; color: black; padding: 10px; margin: 0;">NAN Portal Resources</h2>[[File:Menu-bar.png|thumb|Collapsible menu bar|229x229px]]<p style="margin: 0; padding: 10px 0;">The [https://usnan.org '''NAN portal'''] is composed of a '''Resource Connector''' which is accessible publicly as well as pages requiring an NMRhub account for access. See the [[Creating an Account]] page for how to create an account and the [[User Roles and Permissions]] page for a full list of user roles. The NAN Resources for authenticated users are itemized in a collapsible menu on the left hand side of the web-portal and organized as follows:</p>
* '''[[Resource Connector]]''' (publicly accessible content)
** '''[[Facilities]]''' (list of facility nodes connected to NAN with details such as a description, contacts, addresses, instruments, and services)
** '''Instruments''' (list of instruments from the facility nodes that are a part of the NAN Network)
** '''[[Knowledgebases]]'''
*** [[Knowledgebases for Non-Experts|'''Knowledgebases for non-Experts''']] (concise overviews for newcomers that explain how NMR can address specific research questions, with links to related literature vignettes and Expert KBs)
*** [[Knowledgebase Datasets|'''Knowledgebase Datasets''']] (exemplar datasets with step-by-step protocols and/or analysis scripts that cover sample preparation, experimental setup, signal processing, and data analysis)
*** [[Materials Periodic Table|'''Materials Periodic Table''']] (interactive periodic table to explore the feasibility of utilizing NMR in materials science)
** [[Vignette Library|'''Vignette Library''']] (brief synopses of peer-reviewed studies where NMR played a key role, helping novice users appreciate the technique’s utility and a place to "advertise" publications utilizing NMR)
** [[Public and Publishing|'''Public & Published''']] datasets and collections
* [[Facility Dashboards|'''Facility Dashboards''']] (only visible / accessible by NMR facility managers and staff and used to enter facility and instrument information as well as management of NDTS user settings)
* '''Operations Dashboards'''
* [[Data Browser|'''Data Browsers''']] (accessible to authenticated NMRhub users for viewing datasets, samples, collections, and their permissions)
* [[UHF Access|'''UHF Access''']] (accessible to authenticated NMRhub users to request access to ultra-high-field (UHF) instruments including two 1.1 GHz NAN spectrometers at NMRAM (solids) and CCRC (solutions)
* [[Lab Administration|'''Lab Administration''']] (accessible by PIs and PI delegates to manage lab members, permissions, projects, and funding)<br />
</div>

<div class="nan-box" style="border: 2px solid #444; background: #F3EEFA; padding: 10px; margin-bottom: 15px;">
<h2 class="nan-title" style="background: #C8B9EC; color: black; padding: 10px; margin: 0;">NAN Data Transport System (NDTS)</h2>
<p style="margin: 0; padding: 10px 0;">
NDTS is a system for automatically harvesting data from NAN connected spectrometers to the central NAN archive. NDTS is comprised of a Daemon and lightweight GUI installed on the spectrometer workstations, Gateway software running on a dedicated computer within the NMR facility, and a Receiver and Parser running within the NAN datacenter. NMR facility staff manage the NDTS settings for users through the NAN portal and can adjust NDTS settings through configuration files. Harvested datasets are viewable in the Dataset Browser by those with proper permissions set by PIs as well as facility managers have access to all data collected in their facility.
</p>
<p style="margin: 0; padding: 0px 0;">
See the [[NAN Data Transport System|'''NDTS Documentation''']] for detailed information on NDTS installation, configuration, usage, troubleshooting, and detailed explanation on how NDTS functions.
</p>
</div>

<div class="nan-box" style="border: 2px solid #444; background: #FFF5E5; padding: 10px;">
<h2 class="nan-title" style="background: #FFC266; color: black; padding: 10px; margin: 0;">Help & Support</h2>

==== Support Tickets ====
Support tickets may be created from within the NAN Portal by:

* Selecting the NMRhub widget in the top right corner of all NAN portal pages. From the widget enter your ''Email Address'' (only needed if not logged in with an NMRhub account), enter your ''Message'', and selecting ''Submit''.
** This is the preferred method as it allows us to track the page where you are having issues.
* Support tickets may also be generated by sending an email to [mailto:support@usnan.org support@usnan.org]

==== [[Frequently Asked Questions|FAQ]] ====
A FAQ page on this wiki provides answers to frequently asked questions

==== Wiki Documentation ====
This wiki provides the written documentation for the NAN portal and NDTS. It is intended to be community driven and any NMRhub user may login using the ''login'' link in the upper right hand corner to make edits or create new pages.
</div>