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Chandu Nainala

03.02.2022

nmrXiv

NMR REPOSITORY

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Accelerate broader coordination and data sharing among researchers by creating a computational platform for the management, sharing, and analysis of NMR data.

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https://dev.nmrxiv.org

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An open cloud-based FAIR, consensus-driven data repository to host raw and processed NMR data, with support for browsing, searching, analyzing and disseminating data worldwide.

Journal of Natural Products 2023 – New NMR Data Requirements recommends NMR data deposition in nmrXiv for new compounds reported in J. Nat. Prod. Articles.

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https://nmrxiv.org

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F E A T U R E S

O V E R V I E W

  • Schema
    • ISA Framework
      • Investigation, Study
      • Sample - synthetic / biological
      • Assay
    • Spectra
      • IUPAC - FAIR Spec

Exporters:

Compatibility with DataCite & OpenAIRE Schemas

  • FAIR
  • Data Archival (BagIt)
  • Data formats and Conversions
  • JCAMP-DX, NMReData, nmrML and more industry

oriented formats such as Allotrope Data Format (ADF)

  • Support for Data Versioning / DOI
  • Ontology driven

ISA Specifications (Models)

nmrXiv models (extends ISA)

https://isa-tools.org/

https://github.com/IUPAC/IUPAC-FAIRSpec

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integrations

nmrXiv Core

A R C H I T E C T U R E

O V E R V I E W

Web Application

Application Database

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NMR Database

Search

Importers /

Exporters

Cache

SPA

Front end

File format converters

AI/ML

Tools

API

Workflows

Plugins

OAuth ~ SSO / AAI

ELN

Workflow Dispatcher

https://docs.google.com/presentation/d/1GxKBVx5Hum8I4FH8---4Cu1aZcRYFFAb_YeLLNRcQMM/edit?usp=sharing

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T E C H S T A C K

O V E R V I E W

Web application framework - PHP (MIT)

Database

Cache

Search

Testing

CI/CD

Kubernetes - Helm charts

GKE Ingress / Nginx ~ HTTP reverse proxy / load balancer

Selenium ~ Chrome Driver

Production

Deployment / Testing (Maintenance)

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C U R R E N T S T A T U S

A C T I V E D E V E L O P M E N T

Currently in pre-beta development stage

(Soon to enter beta phase)

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Code base: https://github.com/NFDI4Chem/nmrxiv

Documentation: https://github.com/NFDI4Chem/nmrxiv-docs

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Full Presentation: https://docs.google.com/presentation/d/1GxKBVx5Hum8I4FH8---4Cu1aZcRYFFAb_YeLLNRcQMM/edit?usp=sharing

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Developed alongside with other repositories

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  • msrXiv (Mass Spectrometry)
  • VibSpecDB (Raman)

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C U R R E N T S T A T U S

PROJECTS AND STUDIES

C U R R E N T S T A T U S

P R O J E C T A N D S T U D I E S

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C U R R E N T S T A T U S

AUDITING AND SHARING FEATURES

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C U R R E N T S T A T U S

A U D I T I N G A N D A C C E S S M A N A G E M E N T

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C U R R E N T S T A T U S

C U R R E N T S T A T U S

F I L E U P L O A D

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C U R R E N T S T A T U S

D O C S S I T E

https://docs.nmrxiv.org/docs/developer-guides/installation/development

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Helm Repo - https://github.com/NFDI4Chem/repo-helm-charts

Published - https://nfdi4chem.github.io/repo-helm-charts

D E P L O Y M E N T

K8S H E L M C H A R T S

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O N G O I N G W O R K

D EV E L O P M E N T , S C H E M A S, S T A N D A R D S

  • Versioning

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  • NMRium integration - https://www.nmrium.org/

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  • Schemas

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  • Work flows - Importers/Exporters integration, Converter

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  • Metadata - Ontologies

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  • Testing

Detailed overview: https://docs.google.com/presentation/d/1GxKBVx5Hum8I4FH8---4Cu1aZcRYFFAb_YeLLNRcQMM/edit?usp=sharing

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Thank you

Contact: chandu.nainala@uni-jena.de

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Our team

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Nisha Sharma

Noura Rayya

Christoph Steinbeck

Christian Popp

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Darina Storozhuk

Nazar Stefaniuk

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David Rauh

Steffen Neumann

Tillman Fischer

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Stefan Kuhn