Network for Advanced NMR - User contributions [en]

Feature Summary

2025-07-29T16:29:47Z

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== '''Knowledgebase (KB) Learning Resources''' ==
* '''Novice KBs''' – Primers covering the use of NMR across diverse disciplines including proteins, nucleic acids, materials and chemistry, metabolomics, and other biological samples.
* '''Expert KB datasets''' – Exemplar datasets on test samples with well vetted pulse programs and supplemented with protocols for sample preparation, experimental setups, data processing, and analysis along with processing scripts and processed data.
* '''Vignette library''' – Community-driven summaries of published NMR studies showcasing real-world applications.
* '''Materials Periodic Table''' – Interactive periodic table to explore the feasibility of utilizing NMR of different isotopes in materials science.

== '''Facilities and Instruments''' ==
* '''Ultra-High-Field (UHF) NMR spectrometers''' – Open-access to two 1.1 GHz NMR instruments: one for solids (NMRFAM), one for solutions (CCRC)
* '''Facilities''' – Views of all facilities connected to the NAN network including their instruments and services
* '''Instruments''' – Filterable and sortable tables that list all spectrometers, and probes, connected to the NAN network
* '''UHF access request system''' – Structured, review-based workflow to request access to NAN’s two 1.1 GHz spectrometers and other UHF assets that choose to utilize the UHF request system.

== '''Data Transport & Management''' ==
* '''NDTS (NAN Data Transport System)''' – automated pipeline that harvests raw experiment data from spectrometer workstations to the central archive with rich metadata linking (facility, spectrometer, probe, user, project, study, sample, experimental parameters, etc.).
* '''Manual Dataset Upload''' - ability to bulk upload datasets from a NAN connected spectrometer prior to NDTS installation.
* '''Secure Archival''' – NAN harvested datasets are stored on an enterprise-class network attached storage device and backed up to a geo-dispersed WORM enabled S3 bucket with high data durability. The NAN database is replicated across two datacenters and backed up daily.
* '''Data Browsers''' – Suite of tables for viewing and managing '''''datasets''''', '''''samples''''', and '''''collections'''''. Tables are customizable and each column may be filtered and sorted allowing for powerful queries. Standard and user-defined filters provide quick access to common views. A context menu allows easy access to '''''actions'''''.
* '''Actions''' – Actions allow datasets to be viewed/edited, reassigned, downloaded, pushed to NMRbox, linked to samples, and annotated with classifications, tags, and notes. Actions work with multi-select for efficiency.
* '''Supplemental Data''' – Supplemental data may be added to datasets with a defined category and type (URL, unique identifier, file in dataset, uploaded file).
* '''Sample Definitions''' – Tools to define samples across a wide range of disciplines with tabs for defining the sample '''''description''''', '''''container''''', '''''composition''''', and '''''properties'''''. Sample components are defined by '''''type''''', '''''role''''', '''''quantity''''', and '''''isotopic labeling''''' with additional details based on component type (protein, chemical formula, carbohydrate, mixtures, polymers, etc.). Tools exist for creating sets of samples for environmental and metabolomics, and an interaction manager allows component interactions to be defined.
* '''Organization''' – All lab datasets are accessible from a single view. Hierarchical structure (Projects > Studies > Collections) mirrors a file system for lab data. User collections supported.
* '''Navigation Bar''' – Sidebar enables switching between public, KB, lab/personal, and all datasets & samples.

== '''Public and Published Datasets''' ==
* '''Public datasets''' – Datasets may be marked public anytime and automatically become public three years after harvesting. Release dates may be extended in one-year blocks.
* '''Published datasets & collections''' – Immutable copies of datasets with persistent unique identifier (PUI). Datasets may be published independently or as part of a published collection.

== '''Lab Administration''' ==
* '''Principal Investigators (PIs)''' – PIs in NAN are vetted and act as stewards to data collected by their lab members.
* '''Projects, Studies, Collections & Funding''' – Projects are defined at the lab level and provide three-level hierarchy for organizing lab data. Projects allow fine-grained permissions.
* '''Funding Sources''' – Funding sources are easily added with auto-population for some funding sources.
* '''Permissions''' – Intuitive matrix for controlling lab permissions for current and past users along with collaborators. Lab group defaults allow easy management.
* '''PI Delegate''' – PI delegates act on behalf of the PI reducing administrative burden.

== '''Facility Management''' (viewable by Facility managers and staff) ==
* '''Facility Dashboards''' – Form tools for entering facility, spectrometer, and probe information.
* '''User Management''' – Tools to add users, map local spectrometer users to NAN users, configure default NDTS harvesting for users.
* '''Full Access to Data''' – Facility managers act as stewards of datasets collected in their facility and have the privileges to view, reassign, and purge data.
* '''NDTS''' '''Software''' – Access to download NDTS software and a portal tool for defining NDTS filter settings.

== '''virtual Network Operations Center (vNOC)''' ==
* [[User Roles and Permissions|Role-based]] dashboards with increasing scope:
** '''Public View''' – aggregates data across facilities, instruments, users, and harvested datasets.
** '''PI/User View''' – breaks those metrics down for the lab and individual.
** '''Facility/Administrator View''' – layers on spectrometer uptime, harvesting status, and storage metrics for individual facilities or the whole network, for NAN administrators.
** '''UHF Dashboard''' - accessible by UHF committee members and administrators - provides UHF statistics for submissions based on instrument and submitter

== '''Help & Support''' ==
* '''FAQs''' – Quick answers to common questions.
* '''Wiki''' – Community-editable documentation on the portal and NDTS.
* '''Support tickets''' – Submit through the portal or email (support@usnan.org).

File:KB-materials.png

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KB Dataset Navigation

Knowledgebase Datasets

2025-06-18T13:56:07Z

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== Overview ==
Knowledgebase (KB) Datasets are exemplar experimental datasets collected on test samples at high- and ultra-high magnetic fields. Each dataset provides a vetted pulse program along with all required files to reproduce the experiment and adapt it to other instruments or research samples.

== Contents of a KB Dataset ==
* '''Pulse programs'''
* '''Parameter files'''
* '''Waveform files'''
* '''Time-domain data'''
* '''Sample metadata'''
* '''Protocols'''
** Sample preparation
** Instrument setup
** Experiment setup
** Data processing
** Data analysis
* '''Processing scripts'''
* '''Processed data'''

== Access ==
KB Datasets are '''publicly available''' to all users, whether logged in or not, from the NAN Dataset Browser.

[[File:KB-dataset-menu.png|thumb|KB Dataset navigation]]

* For non-authenticated users: navigate to '''Public Datasets''' from the '''Resource Connector'''. Then select '''Knowledgebase Datasets''' from the left-hand navigation bar.
* For authenticated users: navigate to '''Data Browsers → Datasets''', then select '''Knowledgebase Datasets''' from the left-hand navigation bar.
Datasets may be explored from the Dataset Browser and downloaded via the context menu (right mouse click).

== Navigation ==
KB Datasets are grouped into four main categories:

* Bio Solids
* Materials Solids
* Bio Solution
* Metabolomics

Each category is subdivided up to two additional levels. Selecting a higher-level entry in the hierarchy displays all datasets beneath it, enabling intuitive exploration.

== Sorting and Filtering ==
Columns in the Dataset Browser are sortable. Authenticated users may customize which columns are shown; non-authenticated users are presented with a standard set.

You may also filter on the '''KB''' column from the '''All Datasets''' or '''All Public Datasets''' views to locate KB Datasets.

Knowledgebase Datasets

2025-06-18T13:52:44Z

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== Overview ==
Knowledgebase (KB) Datasets are exemplar experimental datasets collected on test samples at high- and ultra-high magnetic fields. Each dataset provides a vetted pulse program along with all required files to reproduce the experiment and adapt it to other instruments or research samples.

== Contents of a KB Dataset ==
* '''Pulse programs'''
* '''Parameter files'''
* '''Waveform files'''
* '''Time-domain data'''
* '''Sample metadata'''
* '''Protocols'''
** Sample preparation
** Instrument setup
** Experiment setup
** Data processing
** Data analysis
* '''Processing scripts'''
* '''Processed data'''

== Access ==
KB Datasets are '''publicly available''' to all users, whether logged in or not.

[[File:KB-dataset-menu.png|thumb|KB Dataset navigation]]

* For non-authenticated users: navigate to '''Public Datasets''' from the '''Resource Connector'''. Then select '''Knowledgebase Datasets''' from the left-hand navigation bar.
* For authenticated users: navigate to '''Data Browsers → Datasets''', then select '''Knowledgebase Datasets''' from the left-hand navigation bar.

== Navigation ==
KB Datasets are grouped into four main categories:

* Bio Solids
* Materials Solids
* Bio Solution
* Metabolomics

Each category is subdivided up to two additional levels. Selecting a higher-level entry in the hierarchy displays all datasets beneath it, enabling intuitive exploration.

== Sorting and Filtering ==
Columns in the Dataset Browser are sortable. Authenticated users may customize which columns are shown; non-authenticated users are presented with a standard set.

You may also filter on the '''KB''' column from the '''All Datasets''' or '''All Public Datasets''' views to locate KB Datasets.

Knowledgebase Datasets

2025-06-18T13:52:29Z

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== Overview ==
Knowledgebase (KB) Datasets are exemplar experimental datasets collected on test samples at high- and ultra-high magnetic fields. Each dataset provides a vetted pulse program along with all required files to reproduce the experiment and adapt it to other instruments or research samples.

=== Contents of a KB Dataset ===
* '''Pulse programs'''
* '''Parameter files'''
* '''Waveform files'''
* '''Time-domain data'''
* '''Sample metadata'''
* '''Protocols'''
** Sample preparation
** Instrument setup
** Experiment setup
** Data processing
** Data analysis
* '''Processing scripts'''
* '''Processed data'''

== Access ==
KB Datasets are '''publicly available''' to all users, whether logged in or not.

[[File:KB-dataset-menu.png|thumb|KB Dataset navigation]]

* For non-authenticated users: navigate to '''Public Datasets''' from the '''Resource Connector'''. Then select '''Knowledgebase Datasets''' from the left-hand navigation bar.
* For authenticated users: navigate to '''Data Browsers → Datasets''', then select '''Knowledgebase Datasets''' from the left-hand navigation bar.

== Navigation ==
KB Datasets are grouped into four main categories:

* Bio Solids
* Materials Solids
* Bio Solution
* Metabolomics

Each category is subdivided up to two additional levels. Selecting a higher-level entry in the hierarchy displays all datasets beneath it, enabling intuitive exploration.

== Sorting and Filtering ==
Columns in the Dataset Browser are sortable. Authenticated users may customize which columns are shown; non-authenticated users are presented with a standard set.

You may also filter on the '''KB''' column from the '''All Datasets''' or '''All Public Datasets''' views to locate KB Datasets.

Knowledgebase Datasets

2025-06-18T13:50:06Z

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== Overview ==
KB Datasets are exemplar experimental datasets, collected on test samples, designed to guide users through implementation on samples ???. The pulse programs are well vetted and include all the necessary files necessary to run the experiment including protocols for all aspects of experiment setup

KB Datasets contain:
* Pulse programs
* Parameter files
* Waveform files
* Time-domain data
* Sample metadata
* Protocols
** Sample preparation
** Instrument setup
** Experiment setup
** Data processing
** Data analysis
* Processing scripts
* Processed data

== Access ==
The KB Datasets are Public and are available to all users (those logged in or not).
[[File:KB-dataset-menu.png|thumb|KB Dataset Navigation]]
For non-authenticated users navigate to Public Datasets from the Resource Connector. Then select Knowledgebase Datasets from the navigation bar on the left hand side

For authenticated user navigate to the Data Browsers --> Datasets and select Knowledgebase Datasets from the navigation bar on the left hand side

== Navigation ==
KB Datasets are divided into four main categories:

* Bio Solids
* Materials Solids
* Bio Solution
* Metabolomics

Each of the four main categories are further divided into sub-categories two levels deep. This allows easy navigation across all the KB datasets. Note that highlighting a higher level in the hierarchal view will show all datasets underneath from that point.

Sorting and Filtering

Each of the columns in the Dataset Browser are sortable and editable. Authenticated users may customize columns, but for non-authenticated users a defined list of columns are presented.

Note that from the Dataset Browser, All Datasets or All Public Datasets you may filter on the KB column to locate KB Datasets as well.

== Overview ==
Knowledgebase (KB) Datasets are exemplar experimental datasets collected on standardized test samples at high- and ultra-high magnetic fields. Each dataset provides a vetted pulse program along with all required files to reproduce the experiment and adapt it to other instruments or research samples.

=== Contents of a KB Dataset ===
* '''Pulse programs'''
* '''Parameter files'''
* '''Waveform files'''
* '''Time-domain data'''
* '''Sample metadata'''
* '''Protocols'''
** Sample preparation
** Instrument setup
** Experiment setup
** Data processing
** Data analysis
* '''Processing scripts'''
* '''Processed data'''

== Access ==
KB Datasets are '''publicly available''' to all users, whether logged in or not.

[[File:KB-dataset-menu.png|thumb|KB Dataset navigation]]

* For non-authenticated users: navigate to '''Public Datasets''' from the '''Resource Connector'''. Then select '''Knowledgebase Datasets''' from the left-hand navigation bar.
* For authenticated users: navigate to '''Data Browsers → Datasets''', then select '''Knowledgebase Datasets''' from the left-hand navigation bar.

== Navigation ==
KB Datasets are grouped into four main categories:

* Bio Solids
* Materials Solids
* Bio Solution
* Metabolomics

Each category is subdivided up to two additional levels. Selecting a higher-level entry in the hierarchy displays all datasets beneath it, enabling intuitive exploration.

== Sorting and Filtering ==
Columns in the Dataset Browser are sortable. Authenticated users may customize which columns are shown; non-authenticated users are presented with a standard set.

You may also filter on the '''KB''' column from the '''All Datasets''' or '''All Public Datasets''' views to locate KB Datasets.

Knowledgebase Datasets

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Knowledgebases for Non-Experts

2025-06-18T13:43:25Z

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== [https://usnan.nmrhub.org/resource-connector/knowledgebases Overview] ==
[[File:Novice-KBs.png|thumb|Knowledgebases for Non-Experts filtered on ''Materials and Chemistry'']]

[https://usnan.nmrhub.org/resource-connector/knowledgebases KBs for Non-Experts] are organized into '''Content Areas''', with each content area belonging to one or more filterable high-level '''Categories'''

== Categories ==
* '''Proteins'''
* '''Nucleic Acids'''
* '''Materials and Chemistry'''
* '''Metabolomics'''
* '''Other Biological Samples'''

== Content Areas ==
Each Knowledgebase for Non-Experts is organized into '''Content Areas''', which serve as the primary hubs for exploring how NMR can be applied to specific types of samples or scientific questions.

Each '''Content Areas''' belong to one or more '''Categories''' and can be filtered by selecting one or more categories. Note that when no '''Categories''' are selected ''All'' content areas are displayed.

The table below shows the '''Content Areas''' separated by their '''Categories.'''

''If you would like to contribute to these KB Content Areas, please reach out to any of the [https://usnan.org/about/contacts NAN contacts]''
{| class="wikitable"
! Proteins !! Nucleic Acids !! Materials and Chemistry !! Metabolomics !! Other Biological Samples
|-
| Intrinsically Disordered Proteins || DNA || Molecular Crystals || Biomarkers || Biomaterials
|-
| Soluble Proteins || RNA || Glasses and Ceramics || Flux || Carbohydrates
|-
| Fibrils and Polymeric Proteins || || Energy Materials || Compound Identification || Natural Products
|-
| Membrane Proteins || || Synthetic Polymers || Systems Biology ||
|-
| Ligand Binding || || Biomaterials || ||
|-
| || || Catalytic Materials || ||
|-
| || || Surface Chemistry || ||
|-
| || || Organic-Inorganic Hybrids || ||
|-
| || || Metals and Intermetallics || ||
|-
| || || Small Molecules || ||
|}

=== Structure of a Content Area ===
* Each Content Area is composed of a series of '''tabs''' across the top of the page.
** Every Content Area includes a tab titled '''Introduction'''
** Some Content Areas also include a tab titled '''What's right for you?'''
*** This tab walks users through a decision tree to help them determine:
**** If their system is suitable for NMR study
**** What types of NMR experiments are appropriate for their needs

=== Components of Each Tab ===

Each tab may contain the following elements:

* '''HTML blurb'''
** Provides a narrative related to the topic
* '''Links to primary citations'''
** Key references relevant to the scientific subject
* '''Links to related vignettes'''
** '''Content vignettes''' – supplementary pages with in-depth information that does not fit within the main tab layout
** '''Literature vignettes''' – concise summaries of published studies where the topic played a central role
* '''Links to related KB datasets'''
** Direct access to experimental datasets that are well vetted and connected to the subject matter
* '''Image'''
** A representative figure or illustration

User Roles and Permissions

2025-06-13T20:09:23Z

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== NAN Users and NMRbox Users and NMRhub Users—Oh My! ==

* [https://nmrbox.nmrhub.org/ NMRbox] and NAN were both developed at [https://health.uconn.edu/ UConn Health] and operate on shared computational resources hosted by the [https://health.uconn.edu/high-performance-computing/ HPC facility]. NMRbox has served the NMR community for over a decade, during which users had '''NMRbox''' accounts.
* With the introduction of NAN, we wanted to avoid '''YAUA''' — ''Yet Another User Account''. To streamline access, we created the '''[https://nmrhub.org/ NMRhub]''' landing site, which provides links to all computational resources hosted at UConn Health. At the same time, we rebranded NMRbox accounts as '''NMRhub users'''.
* As a result, there is no functional difference between a NAN user and an NMRbox user — throughout the documentation, the terms '''NAN user''' and '''NMRhub user''' are used interchangeably.

<big>'''The Role of Vetted PIs'''</big>

A key change introduced with NAN was the concept of '''vetted PIs''' and the formal linking of users to PI-led lab groups. Previously, users self-declared their roles (e.g., PI, graduate student), but these designations were not verified.

Because '''dataset ownership in NAN is PI-based''', we added mechanisms for:
* Users to update their account and request '''PI status'''
* The NAN team to verify and approve PI status
* Users to request access to a PI's lab group, which must be approved by the PI or their delegate
<big>'''Seamless Access Through SSO'''</big>

We have implemented '''Single Sign-On (SSO)''' across all NMRhub resources — including '''NMRbox''', '''NAN''', '''[https://nuscon.org/home NUScon]''', and the '''virtual NAN Operations Center''' — to enable seamless navigation and access across the ecosystem.

== Public User ==
A user who is not authenticated with an NMRhub account.

They have view-only access to:
* The '''[[Resource Connector]]''' (lists facilities, instruments, configurations, searchable by services)
* The '''Knowledgebase''' (introductory content on how NMR can be used in research)
* The '''Vignette Library''' (summaries of papers using NMR)
* The '''Materials Periodic Table''' (isotope-specific NMR attributes)
* All '''Public Datasets''' including those in the Knowledgebase
* '''Published Collections'''
* The '''[https://usnan.nmrhub.org/operations/kibana-public Public View]''' of the Virtual NAN Operations Center (vNOC)

== Standard NAN User ==
An authenticated user with an NMRhub account.

They have access to:
* All Public User content
* '''Dataset, Sample, and Collection Browsers''' (for data they have permission to see)
* The ability to '''reassign datasets''' to other lab members for 3 months after harvesting
* '''UHF Access''' (view/submit requests if granted by their PI)
* '''My Permissions''' (shows what permissions their PI has granted)
* The '''[https://usnan.nmrhub.org/operations/kibana-user User Dashboard]''' of vNOC
* The ability to create '''Literature Vignettes'''

== Principal Investigator (PI) ==
Includes everything a standard NAN User sees, plus:
* Access to '''[[Lab Administration]]''' for:
** Creating and managing Projects
** Adding funding sources
** Managing lab users and permissions
* The '''[https://usnan.nmrhub.org/operations/kibana-pi PI Dashboard]''' of vNOC (summary of lab-wide data)
* Ability to create '''Literature Vignettes'''

== PI Delegate ==
A lab-group member designated by the PI with delegate permissions.

* Can switch into the PI account to perform actions on their behalf (like the ''su'' command in Linux)
* Does not have PI privileges in their own account directly
* All actions are performed as the PI once switched

== Facility Manager (Staff) ==
A user designated as staff for an NMR facility.

They have:
* Access to the '''[[Facility Dashboards|Facility Dashboard]]''' for:
** Editing facility, instrument, and probe details
** Managing users and instrument records
** Downloading NDTS software
* Real-time updates to the portal based on dashboard changes
* Unrestricted access to all datasets collected within their facility
* Ability to '''reassign''' or '''purge datasets collected within their facility'''
* The '''[https://usnan.nmrhub.org/operations/kibana-fm Facility Dashboard]''' of vNOC

== Knowledgebase / Website Content Provider ==
A NAN user with content editing privileges.

They can:
* Create and edit '''Knowledgebase content'''
* Assign datasets as '''KB Datasets'''
* Edit any page with built-in content management tools on the portal

== UHF Reviewer ==
A user added to the reviewer pool for Ultra-High Field (UHF) requests.

* All PIs from labs with access to 1.1 GHz instruments are automatically added

== UHF Administrator ==
A privileged user who helps run the UHF system.

* Has full access to manage UHF requests
* Assists the UHF Operations Committee and current cycle chair

== UHF Operations Committee Member ==
A user with broad oversight of UHF review activities.

They can:
* Manage and review UHF requests
* Assign reviewers
* Modify user roles and expertise areas
* Change the status of UHF requests
* One member serves as the '''Chair''' for each review cycle

User Roles and Permissions

2025-06-13T20:03:55Z

Mtest: /* NAN users and NMRbox users and NMRhub users—oh my! */

== NAN users and NMRbox users and NMRhub users—oh my! ==
NMRbox and NAN were both developed at UConn Health on shared computational resources operating out of the HPC facility. NMRbox has been utilized by the NMR community for over a decade and users had "NMRbox" accounts. With the introduction of NAN we did not want YAUA—Yet Another User Account. We decided to create the NMRhub landing space with links to the computational resources hosted at UConn Health and rebranded NMRbox users as NMRhub users. Thus, there is no difference between a NAN user or NMRbox user and we call them "NMRhub users". Throughout the wiki documentation the terms NAN user and NMRhub user are used interchangeably.

One key change in NMRhub user accounts was made with the introduction of NAN and that was the concept of vetted PIs and the linking of users to PIs. In the past we let users self-declare if they were a PI, graduate student, etc., but those designations were not vetted. As dataset ownership in NAN is based on PIs we added the ability for users to update their accounts and request PI status. We verify the PI status and then approve the change to the account. We also created the ability for users to request access to a PIs lab-group which must be approved by the PI or their delegate.

We have implemented SSO across NMRhub resources (NMRbox, NAN, NUScon, NMRhub, and the NAN virtual NAN operations center) for seamless navigation between them.

== NAN Users and NMRbox Users and NMRhub Users—Oh My! ==

NMRbox and NAN were both developed at UConn Health and operate on shared computational resources hosted by the HPC facility. NMRbox has served the NMR community for over a decade, during which users had '''NMRbox''' accounts.

With the introduction of NAN, we wanted to avoid '''YAUA''' — ''Yet Another User Account''. To streamline access, we created the '''NMRhub''' landing site, which provides links to all computational resources hosted at UConn Health. At the same time, we rebranded NMRbox accounts as '''NMRhub users'''.

As a result, there is no functional difference between a NAN user and an NMRbox user — throughout the documentation, the terms '''NAN user''' and '''NMRhub user''' are used interchangeably.

=== The Role of Vetted PIs ===

A key change introduced with NAN was the concept of '''vetted PIs''' and the formal linking of users to PI-led lab groups. Previously, users self-declared their roles (e.g., PI, graduate student), but these designations were not verified.

Because '''dataset ownership in NAN is PI-based''', we added mechanisms for:
* Users to update their account and request '''PI status'''
* The NAN team to verify and approve PI status
* Users to request access to a PI's lab group, which must be approved by the PI or their delegate

=== Seamless Access Through SSO ===

We have implemented '''Single Sign-On (SSO)''' across all NMRhub resources — including '''NMRbox''', '''NAN''', '''NUScon''', and the '''virtual NAN Operations Center''' — to enable seamless navigation and access across the ecosystem.

== Public User ==
A user who is not authenticated with an NMRhub account.

They have view-only access to:
* The '''[[Resource Connector]]''' (lists facilities, instruments, configurations, searchable by services)
* The '''Knowledgebase''' (introductory content on how NMR can be used in research)
* The '''Vignette Library''' (summaries of papers using NMR)
* The '''Materials Periodic Table''' (isotope-specific NMR attributes)
* All '''Public Datasets''' including those in the Knowledgebase
* '''Published Collections'''
* The '''[https://usnan.nmrhub.org/operations/kibana-public Public View]''' of the Virtual NAN Operations Center (vNOC)

== Standard NAN User ==
An authenticated user with an NMRhub account.

They have access to:
* All Public User content
* '''Dataset, Sample, and Collection Browsers''' (for data they have permission to see)
* The ability to '''reassign datasets''' to other lab members for 3 months after harvesting
* '''UHF Access''' (view/submit requests if granted by their PI)
* '''My Permissions''' (shows what permissions their PI has granted)
* The '''[https://usnan.nmrhub.org/operations/kibana-user User Dashboard]''' of vNOC
* The ability to create '''Literature Vignettes'''

== Principal Investigator (PI) ==
Includes everything a standard NAN User sees, plus:
* Access to '''[[Lab Administration]]''' for:
** Creating and managing Projects
** Adding funding sources
** Managing lab users and permissions
* The '''[https://usnan.nmrhub.org/operations/kibana-pi PI Dashboard]''' of vNOC (summary of lab-wide data)
* Ability to create '''Literature Vignettes'''

== PI Delegate ==
A lab-group member designated by the PI with delegate permissions.

* Can switch into the PI account to perform actions on their behalf (like the ''su'' command in Linux)
* Does not have PI privileges in their own account directly
* All actions are performed as the PI once switched

== Facility Manager (Staff) ==
A user designated as staff for an NMR facility.

They have:
* Access to the '''[[Facility Dashboards|Facility Dashboard]]''' for:
** Editing facility, instrument, and probe details
** Managing users and instrument records
** Downloading NDTS software
* Real-time updates to the portal based on dashboard changes
* Unrestricted access to all datasets collected within their facility
* Ability to '''reassign''' or '''purge datasets collected within their facility'''
* The '''[https://usnan.nmrhub.org/operations/kibana-fm Facility Dashboard]''' of vNOC

== Knowledgebase / Website Content Provider ==
A NAN user with content editing privileges.

They can:
* Create and edit '''Knowledgebase content'''
* Assign datasets as '''KB Datasets'''
* Edit any page with built-in content management tools on the portal

== UHF Reviewer ==
A user added to the reviewer pool for Ultra-High Field (UHF) requests.

* All PIs from labs with access to 1.1 GHz instruments are automatically added

== UHF Administrator ==
A privileged user who helps run the UHF system.

* Has full access to manage UHF requests
* Assists the UHF Operations Committee and current cycle chair

== UHF Operations Committee Member ==
A user with broad oversight of UHF review activities.

They can:
* Manage and review UHF requests
* Assign reviewers
* Modify user roles and expertise areas
* Change the status of UHF requests
* One member serves as the '''Chair''' for each review cycle

User Roles and Permissions

2025-06-13T20:02:08Z

Mtest:

== NAN users and NMRbox users and NMRhub users—oh my! ==
NMRbox and NAN were both developed at UConn Health on shared computational resources operating out of the HPC facility. NMRbox has been utilized by the NMR community for over a decade and users had "NMRbox" accounts. With the introduction of NAN we did not want YAUA—Yet Another User Account. We decided to create the NMRhub landing space with links to the computational resources hosted at UConn Health and rebranded NMRbox users as NMRhub users. Thus, there is no difference between a NAN user or NMRbox user and we call them "NMRhub users". Throughout the wiki documentation the terms NAN user and NMRhub user are used interchangeably.

One key change in NMRhub user accounts was made with the introduction of NAN and that was the concept of vetted PIs and the linking of users to PIs. In the past we let users self-declare if they were a PI, graduate student, etc., but those designations were not vetted. As dataset ownership in NAN is based on PIs we added the ability for users to update their accounts and request PI status. We verify the PI status and then approve the change to the account. We also created the ability for users to request access to a PIs lab-group which must be approved by the PI or their delegate.

We have implemented SSO across NMRhub resources (NMRbox, NAN, NUScon, NMRhub, and the NAN virtual NAN operations center) for seamless navigation between them.

== Public User ==
A user who is not authenticated with an NMRhub account.

They have view-only access to:
* The '''[[Resource Connector]]''' (lists facilities, instruments, configurations, searchable by services)
* The '''Knowledgebase''' (introductory content on how NMR can be used in research)
* The '''Vignette Library''' (summaries of papers using NMR)
* The '''Materials Periodic Table''' (isotope-specific NMR attributes)
* All '''Public Datasets''' including those in the Knowledgebase
* '''Published Collections'''
* The '''[https://usnan.nmrhub.org/operations/kibana-public Public View]''' of the Virtual NAN Operations Center (vNOC)

== Standard NAN User ==
An authenticated user with an NMRhub account.

They have access to:
* All Public User content
* '''Dataset, Sample, and Collection Browsers''' (for data they have permission to see)
* The ability to '''reassign datasets''' to other lab members for 3 months after harvesting
* '''UHF Access''' (view/submit requests if granted by their PI)
* '''My Permissions''' (shows what permissions their PI has granted)
* The '''[https://usnan.nmrhub.org/operations/kibana-user User Dashboard]''' of vNOC
* The ability to create '''Literature Vignettes'''

== Principal Investigator (PI) ==
Includes everything a standard NAN User sees, plus:
* Access to '''[[Lab Administration]]''' for:
** Creating and managing Projects
** Adding funding sources
** Managing lab users and permissions
* The '''[https://usnan.nmrhub.org/operations/kibana-pi PI Dashboard]''' of vNOC (summary of lab-wide data)
* Ability to create '''Literature Vignettes'''

== PI Delegate ==
A lab-group member designated by the PI with delegate permissions.

* Can switch into the PI account to perform actions on their behalf (like the ''su'' command in Linux)
* Does not have PI privileges in their own account directly
* All actions are performed as the PI once switched

== Facility Manager (Staff) ==
A user designated as staff for an NMR facility.

They have:
* Access to the '''[[Facility Dashboards|Facility Dashboard]]''' for:
** Editing facility, instrument, and probe details
** Managing users and instrument records
** Downloading NDTS software
* Real-time updates to the portal based on dashboard changes
* Unrestricted access to all datasets collected within their facility
* Ability to '''reassign''' or '''purge datasets collected within their facility'''
* The '''[https://usnan.nmrhub.org/operations/kibana-fm Facility Dashboard]''' of vNOC

== Knowledgebase / Website Content Provider ==
A NAN user with content editing privileges.

They can:
* Create and edit '''Knowledgebase content'''
* Assign datasets as '''KB Datasets'''
* Edit any page with built-in content management tools on the portal

== UHF Reviewer ==
A user added to the reviewer pool for Ultra-High Field (UHF) requests.

* All PIs from labs with access to 1.1 GHz instruments are automatically added

== UHF Administrator ==
A privileged user who helps run the UHF system.

* Has full access to manage UHF requests
* Assists the UHF Operations Committee and current cycle chair

== UHF Operations Committee Member ==
A user with broad oversight of UHF review activities.

They can:
* Manage and review UHF requests
* Assign reviewers
* Modify user roles and expertise areas
* Change the status of UHF requests
* One member serves as the '''Chair''' for each review cycle

Main Page

2025-06-13T19:41:23Z

Mtest:

{{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>
NAN is a collaborative initiative involving the [https://health.uconn.edu/structural-biology/ Gregory P. Mullen Structural Biology Facility] at [https://health.uconn.edu/ UConn Health], the [https://nmr.ccrc.uga.edu/ Complex Carbohydrate Research Center (CCRC)] at [https://www.uga.edu/ UGA], and the [https://nmrfam.wisc.edu/ National Magnetic Resonance Facility at Madison (NMRFAM)] at [https://www.wisc.edu/ UW-Madison]. Its mission is to democratize the utilization of high-field NMR in biomedicine, materials science, and chemistry and provide data stewardship through the NAN Archive. 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.

NAN provides a suite of four Knowledgebases (KBs) in Bio Solids, Material Solids, Bio Solution, and Metabolomics that comprehensively guide novice and expert users through discovering how NMR may be utilized to solvent scientific problems as well as KB datasets with all the resources need to run NMR experiments; sample preparation, vetted pulse programs, experimental setup, and data processing and analysis.

On the portal, dashboards provide tools for (1) facility staff to manage facility information, instruments and probes, and manage facility users, (2) PIs to create projects and manage lab members, and (3) a virtual network operations center for monitoring NAN.

A distinguishing feature is the NAN Data Transport System (NDTS), which 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 own data collected in their lab and control access. Users can create detailed sample records and link samples with datasets.

Interested in having your NMR facility join as a NAN node? Click [[Joining NAN|here]] for more information.

Test
</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 [[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 facilities connected to the NAN Network)
** Instruments (list of instruments connected to the NAN Network)
** Knowledgebases (non-expert content to discover the utility of NMR across a wide range of scientific disciplines)
** Knowledgebase Datasets (well vetted pulse programs with parameter sets, example data, processing scripts, and protocols)
** Materials Periodic Table (to explore the feasibility of utilizing NMR in materials science)
** [[Vignette Library]] (a place to highlight publications utilizing NMR)
** [[Public and Publishing|Public & Published]] datasets and collections
* [[Facility Dashboards]] (only visible / accessible by NMR facility managers and staff)
* Operations Dashboards
* [[Data Browser|Data Browsers]] (accessible to authenticated NMRhub users for viewing datasets, samples, collections, and [[Lab Permissions|permissions]])
* [[UHF Access]] (accessible to authenticated NMRhub users to request access to the two 1.1 GHz NAN spectrometers)
* [[Lab Administration]] (accessible by PIs and PI delegates to manage lab members, permissions, projects, and funding) (Only visible to PIs and PI Delegates)<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 Guide]] 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. However, 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>

Vignette Library

2025-06-13T19:33:28Z

Mtest: /* Overview */

== Overview ==

'''Literature Vignettes''' summarize publications (or unpublished work) that demonstrate how NMR was used to solve scientific problems. These vignettes aim to inform the community by highlighting practical applications of NMR and to help researchers ''"advertise"'' concise summaries of their work with others.

'''Content Vignettes''' are created by users who are designated as KB Content providers and are designed to provide additional information for Novice Knowledgebases.

== Who Can Create Literature Vignettes? ==

Any authenticated user on the NAN web portal can create Literature Vignettes. The goal is for this to become a community-driven resource.

== How to Create a Literature Vignette ==

To create a new vignette:

# Navigate to '''Resource Connector → Vignette Library'''.
# Log in if you are not already
# Click the '''New Vignette''' button
# Fill out the form using the fields below:

{| class="wikitable"
! Field !! Required? !! Description
|-
| '''Type''' || Yes - but only visible for KB Content Providers, all others default to Literature || Choose between '''Literature''' or '''Content'''. Only KB content providers will see this field. Most users will not.
|-
| '''Title''' || Yes || Enter the title of the vignette.
|-
| '''Short Description''' || No || A brief summary shown on the vignette tile.
|-
| '''Vignette Content''' || Yes || Use the editor to write the body of the vignette. Standard formatting and linking options are available.
|-
| '''Vignette Image''' || No || Optionally upload an image to accompany the vignette.
|-
| '''Primary Citation DOI''' || Yes || Click '''Add Row''' to enter citation(s). Each row requires a '''Description''' and a '''Link''' (preferably a DOI or URL).
|-
| '''Related Expert KBs''' || No || Click '''Add Row''' to link related KB datasets. Each row requires a '''Description''' and a '''Link''' to a public or published dataset (use the context menu [right mouse click] in the Dataset Browser to copy the link to the clipboard for pasting).
|-
| '''Related Vignettes''' || No || Click the '''Select Vignettes''' button to choose related vignettes. Use the scroll or search function to locate them.
|}

'''<big>Buttons</big>:'''
* '''Cancel''' – Exits without saving
* '''Save''' – Saves a draft (remains private)
* '''Publish''' – Publishes the vignette for public view (cannot be undone once published)

== Searching & Viewing Vignettes ==

'''<big>Searching</big>'''

A search bar at the top of the Vignette Library allows searching across all vignette content.

'''<big>Viewing</big>'''

* Click the '''eye icon''' on a vignette tile for a preview
* Click the vignette tile to open the full vignette
** Use the '''Previous''' and '''Next''' buttons to navigate through vignettes

== Display Order ==

Vignettes are ordered by creation date, with the most recent appearing at the top. This helps users stay updated with newly added content.

== Why Are Some Vignettes Red? ==

Vignettes that are saved but not yet published appear in '''red'''. Only the creator can view these unpublished drafts.

Main Page

2025-06-13T15:37:19Z

Mtest:

{{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>
NAN is a collaborative initiative involving the [https://health.uconn.edu/structural-biology/ Gregory P. Mullen Structural Biology Facility] at [https://health.uconn.edu/ UConn Health], the [https://nmr.ccrc.uga.edu/ Complex Carbohydrate Research Center (CCRC)] at [https://www.uga.edu/ UGA], and the [https://nmrfam.wisc.edu/ National Magnetic Resonance Facility at Madison (NMRFAM)] at [https://www.wisc.edu/ UW-Madison]. Its mission is to democratize the utilization of high-field NMR in biomedicine, materials science, and chemistry and provide data stewardship through the NAN Archive. 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.

NAN provides a suite of four Knowledgebases (KBs) in Bio Solids, Material Solids, Bio Solution, and Metabolomics that comprehensively guide novice and expert users through discovering how NMR may be utilized to solvent scientific problems as well as KB datasets with all the resources need to run NMR experiments; sample preparation, vetted pulse programs, experimental setup, and data processing and analysis.

On the portal, dashboards provide tools for (1) facility staff to manage facility information, instruments and probes, and manage facility users, (2) PIs to create projects and manage lab members, and (3) a virtual network operations center for monitoring NAN.

A distinguishing feature is the NAN Data Transport System (NDTS), which 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 own data collected in their lab and control access. Users can create detailed sample records and link samples with datasets.

Interested in having your NMR facility join as a NAN node? Click [[Joining NAN|here]] for more information.

Test
</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 [[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 facilities connected to the NAN Network)
** Instruments (list of instruments connected to the NAN Network)
** Knowledgebase Content (non-expert content to discover the utility of NMR across a wide range of scientific disciplines)
** Knowledgebase Datasets (well vetted pulse programs with parameter sets, example data, processing scripts, and protocols)
** Vignette Library (a place to highlight publications utilizing NMR)
** Materials Periodic Table (to explore the feasibility of utilizing NMR in materials science)
** [[Public and Publishing|Public & Published]] datasets and collections
* [[Facility Dashboards]] (accessible by NMR facility managers and staff) (Only visible to users identified as Facility Staff)
* Operations Dashboards
* [[Data Browser|Data Browsers]] (accessible to authenticated NMRhub users for viewing datasets, samples, collections, and [[Lab Permissions|permissions]])
* [[UHF Access]] (accessible to authenticated NMRhub users to request access to the two 1.1 GHz NAN spectrometers)
* [[Lab Administration]] (accessible by PIs and PI delegates to manage lab members, permissions, projects, and funding) (Only visible to PIs and PI Delegates)<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 Guide]] 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. However, 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>