Developing open source software to enable network-based biomedical discovery

The National Resource for Network Biology (NRNB) organizes the development of free, open source software technologies to enable network-based visualization, analysis, and biomedical discovery. Biomedical research is increasingly dependent on knowledge of biological networks of multiple types and scales, including gene, protein and drug interactions, cell-cell and cell-host communication, and vast social networks. Our technologies enable researchers to assemble and analyze these networks and to use them to better understand biological systems and, in particular, how they fail in disease.

The NRNB mentoring organization includes projects such as Cytoscape, WikiPathways, SBML, and cBioPortal. This is a great opportunity to work at the intersection of biology and computing! For example, Cytoscape is downloaded over 16,000 times per month by researchers. We take mentoring seriously and are proud of our >90% success rate with former students and projects. But don't take our word for it, read testimonials from prior NRNB students students and mentors.

Find out more about the software projects being developed in coordination with NRNB. Also refer to the NRNB GSoC 2016 page for additional resources and application tips.

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Technologies

  • c++
  • java
  • javascript
  • php
  • python

Topics

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National Resource for Network Biology (NRNB) 2016 Projects

  • 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...
  • 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...
  • 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...
  • 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...
  • 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...
  • 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 ....
  • 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...
  • Kaito
    Interconvertible Layout program for CellDesigner
    CellDesigner is a modeling/simulating software capable of visualizing, modeling, and simulating gene­regulatory and biochemical networks. The key...
  • 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...
  • 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...
  • 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...
  • 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...
  • 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...
  • 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...
  • 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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2016