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National Resource for Network Biology (NRNB)

The National Resource for Network Biology (NRNB, https://nrnb.org) 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 expressed in terms of networks, including gene, protein and drug interactions, cell-cell and viral-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 (https://cytoscape.org/), WikiPathways (https://wikipathways.org/), SBML (https://sbml.org/), SBGN (https://sbgn.github.io/) and others. This is a great opportunity to work at the intersection of biology and computing! For example, Cytoscape is downloaded over 24,000 times per month by researchers. We take mentoring seriously and are proud of our 96% success rate (https://nrnb.org/alumni.html#gsoc-tab) with former students and projects. But don’t take our word for it, read testimonials from prior NRNB students (https://nrnb.org/testimonials.html#student-tab) and mentors (https://nrnb.org/testimonials.html#mentor-tab). Find out more about the software projects being developed in coordination with NRNB at our website (https://nrnb.org). Also refer to our GSoC page (https://nrnb.org/gsoc.html) for additional resources and application tips.

GSoC Participation History

Technologies

Topics

Past Projects

Implement a Data-Driven Visual Attribute Mapping System in GraphSpace

This project aims to implement a Visual Attribute Mapping System that enables users to automatically map node and edge attributes to visual...

openPIP 2 Modernizing the Open Source Protein Interaction Platform

openPIP is an open-source platform for hosting and visualizing protein-protein interaction (PPI) data. The current version is built on a PHP 5.6 /...

Enhancing VCell AI Platform

VCell-AI is an AI-powered platform for discovering, analyzing, and exploring biological models from the VCell database. While the platform already...

Proposal for the Unified App Registry for Cytoscape App Store

Currently, the Cytoscape App Store only supports plugins for the Cytoscape Desktop App. Since a web version of Cytoscape is available, web plugins...

Evaluating and Improving Symbolic Regression Methods for Biological Network Dynamics

This project aims to improve and evaluate symbolic regression methods for discovering interpretable mathematical models of biological network...

ML Models that use SBOL for DNA annotation by Shreeya

Developing a scalable and reproducible research pipeline within SeqTrainer for bacterial DNA sequence modelling and annotation using SBOL-based...

Direct Integration of PathVisio with WikiPathways GitHub

This project aims to develop a Direct GitHub Integration Plugin for PathVisio to transform the pathway curation workflow from outdated systems to the...

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