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National Resource for Network Biology

Trey Ideker, Ph.D.
P41GM103504
Active

Center Overview

Analysis of biological networks has exploded in recent years. A wide variety of technologies have become available for mapping biological networks at multiple levels and scales, from protein-protein and genetic interactions, to cell-cell communication, to vast social networks. The aim of the National Resource for Network Biology is to develop new algorithms, visualizations, and conceptual frameworks to integrate, query, and interpret these network data. Our technologies are enabling researchers to assemble models of networks and pathways and to use these networks to better understand how biological systems operate and how they fail in disease.

Most diseases are not only complex (driven by a combination of many genes) but also wildly heterogeneous (gene combinations can vary greatly from patient to patient). For this reason, in the search for disease genes it will be crucial to understand the networks in which these genes function. These networks span multiple layers, from molecular interaction networks inside cells to social interaction networks among individuals, pathogens, and the environment. Specific areas in which Network Biology is making an impact are: identification of disease subnetworks, network-based diagnosis, and network-based gene association. Beyond these disease applications, a wide range of computational techniques are being developed in order to analyze biological network data to address specific problems with relevance to basic biology and human health: gene function prediction, detection of protein complexes and other modular structures, network evolution, and prediction of new interactions and functional associations.

Tags

Complex Networks, Computational Modeling, Proteomics Profiling

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
CBio Portal
National Resource for Network Biology
NIGMS

cBio Cancer Genomics Portal provides visualization, analysis and download of large-scale cancer genomics data sets. With NRNB funding, the portal now enables researchers to dynamically visualize, analyze and filter cancer genomic data in the context of pathways and interaction networks derived from Pathway Commons. Network visualization is provided by cytoscape.js.

Web-Based BioPAX N/A N/A
Cytoscape
National Resource for Network Biology
NIGMS

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of experiment data and annotation. A large and growing collection of apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

Linux, Mac OSX, Windows BioPAX, GML, JSON, SBML,...(more) N/A N/A
cytoscape.js
National Resource for Network Biology
NIGMS

Cytoscape.js is a reusable component that allows you to embed networks within HTML documents. It is easily integrated in HTML via its Javascript API and customisable in what data it loads and how it visually displays that data. It is an open source bioinformatics environment for integration, visualization, and query of biological networks that can be used with a broad variety of data types and customized through the use and development of plugin extensions.

Web-Based JSON N/A N/A
Cytoscape App Store
National Resource for Network Biology
NIGMS

The Cytoscape App Store highlights the important features that apps add to Cytoscape, enable researchers to find and install apps they need and help developers promote their apps. Cytoscape provides a solid platform for network visualization and analysis, but it’s really all about the apps. Researchers and developers from institutions around the world have built on top of Cytoscape to add new functionality and tailored solutions for a broad range of network-related projects. The App Store is dedicated to...

Web-Based Database 2GB - 8GB
GeneMANIA
National Resource for Network Biology
NIGMS

GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity.

Web-Based BioPAX Database 2GB - 8GB
NDEx
National Resource for Network Biology
NIGMS

NDEx (the Network Data Exchange) is an open source software platform where scientists and organizations can share, store, manipulate and publish biological network knowledge. Users can take advantage of the free Public NDEx Server while companies and organizations can decide to install their own NDEx Server application locally. The NDEx Project is developed in tight association with the Cytoscape project.

Web-Based JSON Database 2GB - 8GB
NeXO
National Resource for Network Biology
NIGMS

NeXO is a gene ontology inferred directly from large-scale molecular networks. A gene ontology provides structured knowledge about the cellular components, processes, and functions encoded by genes. While most ontologies – including the highly successful Gene Ontology Database (GO) – are constructed through manual expert curation, NeXO is a data-driven gene ontology inferred directly from ‘omics data. NeXO (The Network Extracted Ontology) uses a principled computational approach which integrates evidence from hundreds of thousands of individual...

Web-Based Database 2GB - 8GB
WikiPathways
National Resource for Network Biology
NIGMS

WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. Users can browse and edit pathways of interest from dozens of model organisms and download pathways in several formats.

Web-Based BioPAX, JSON Database 500MB - 2GB