NDEx: Accessing Network Models and Streamlining Network Biology Workflows.
Cytoscape
JavaScript
NDEx
R
REST API
enrichment analysis
neighborhood query
network biology
network models
pathway
python
subnetwork
systems biology
Journal
Current protocols
ISSN: 2691-1299
Titre abrégé: Curr Protoc
Pays: United States
ID NLM: 101773894
Informations de publication
Date de publication:
Sep 2021
Sep 2021
Historique:
entrez:
27
9
2021
pubmed:
28
9
2021
medline:
30
9
2021
Statut:
ppublish
Résumé
NDEx, the Network Data Exchange (https://www.ndexbio.org) is a web-based resource where users can find, store, share and publish network models of any type and size. NDEx is integrated with Cytoscape, the widely used desktop application for network analysis and visualization. NDEx and Cytoscape are the pillars of the Cytoscape Ecosystem, a diverse environment of resources, tools, applications and services for network biology workflows. In this article, we introduce researchers to NDEx and highlight how it can simplify common tasks in network biology workflows as well as streamline publication and access to). Finally, we show how NDEx can be used programmatically via Python with the 'ndex2' client library, and point readers to additional examples for other popular programming languages such as JavaScript and R. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Getting started with NDEx Basic Protocol 2: Using NDEx and Cytoscape in a publication-oriented workflow Basic Protocol 3: Manipulating networks in NDEx via Python.
Identifiants
pubmed: 34570431
doi: 10.1002/cpz1.258
pmc: PMC8544027
mid: NIHMS1740024
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e258Subventions
Organisme : NIGMS NIH HHS
ID : P41 GM103504
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA184427
Pays : United States
Informations de copyright
© 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.