National Resource for Network Biology (NRNB)

Developing open source tools for network biology

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graphics
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network biology
data visualization
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Projects

Contributor

Supun Arunoda

Principal Coordinate Analysis and t-Distributed Stochastic Neighbor Embedding in clusterMaker2

Implement two algorithms which have the ability to do dimensional reduction in cluster Network. Principal Coordinate Analysis and t-Distributed...

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Contributor

jooolia

Enhance vignettes and plugin use for R package RCy3 for network manipulation using Cytoscape

Many scientists use networks to visualize complex relationships among species, people, cities, genes, proteins or other subjects. Cytoscape is...

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Contributor

Istemi Bahceci

Visualizing genomic alterations in TCGA cancer pathways in cBioPortal

The main goal of this project is to provide a new network view which is capable of visualizing curated TCGA pathways that are more attractive and...

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Contributor

Metin Can Siper

Improving Web Based SBGN Editor SBGNViz.js

SBGNViz.js is an open source web application based on Cytoscape.js to visualize the pathway models represented by SBGN Process Description Notation ....

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Contributor

Hovakim Grabski

Java support for Deviser, a code generation system for SBML libraries

Since SBML Level 3 is being developed as a modular format with optional SBML Level 3 packages are available to extend the focus of the core SBML...

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Contributor

MridulS

Import graphs in multiple formats and Cytoscape files into GraphSpace

GraphSpace is a tool for storing, sharing, and visualising graphs in order to help collaborative research. Users can upload graphs and share it with...

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Contributor

Roman Schulte

GSoC: JSBML Validation System

The JSBML library is a powerful Java library that gives the use a easy possibility to read, write and manipulate SBML files with Java. Because there...

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Contributor

Devesh Khandelwal

SBGN-ML and SBML to Escher Converter

Escher is quickly growing in popularity. As Escher currently uses JSON as its data and layout representation format, and most of the community...

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Contributor

Kaito

Interconvertible Layout program for CellDesigner

CellDesigner is a modeling/simulating software capable of visualizing, modeling, and simulating gene­regulatory and biochemical networks. The key...

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Contributor

tramy

Interconversion between the systems biology modeling formats SBML and BioPAX

In the systems biology field, there exists many different standards, with each standard serving for a different purpose. BioPax is a standard used...

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Contributor

ibestvina

Multithread Centiscape (#55)

CentiScaPe is a Cytoscape application used to calculate a number of different node centralities in a network. All of the centrality calculating...

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Contributor

Ashish Tiwari

Cytoscape command line scripting enhancements

Cytoscape is a general purpose, open source software platform for complex network data integration, analysis and visualization. Cytoscape’s core...

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Contributor

MilesGSOC

The Online Resource for Interface Based Interaction Networks (TOR-IBIN) Web Interface

TOR-IBIN will be an online resource for gathering and storing published interface-based protein-protein interactions (PPI). TOR-IBIN aims to make...

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Contributor

joseph.stahl

Tutorials for Cytoscape.js

Tutorials serve as an invaluable way to familiarize oneself with new software. Cytoscape.js currently provides demos but lacks tutorials to tie...

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Contributor

Zhaoyuan Zoe Xi

Extending Cytoscape.js: Addition of Clustering Algorithms

Cytoscape.js is a graph theory and networks library focused on providing built-in, rich and performant graph models for analysis and data...

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