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 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, WikiPathways, SBML, and cBioPortal. This is a great opportunity to work at the intersection of biology and computing! For example, Cytoscape is downloaded over 18,000 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 page for additional resources and application tips.

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Technologies

  • java
  • javascript
  • python
  • r
  • rest

Topics

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National Resource for Network Biology (NRNB) 2020 Projects

  • Rahul Agrawal
    Adding Bio-Statistical Machine Learning Models and Graphical visualization to ABioTrans V2
    ABioTrans is a bio-statistical/informatics tool, developed in R for gene expression analysis. The tool allows the user to directly read RNA-Seq data...
  • Maija Utriainen
    Developing a tool for implementing clustering algorithms to Cytoscape app ClusterMaker2
    In this project, I will develop a tool in Cytoscape app ClusterMaker2 that helps implementing new clustering algorithms in the app from inside...
  • Medha Bhattacharya
    Development of a system that generates spatial SBML models using deep learning
    This project aims at creating and implementing a system that automatically generates various spatial SBML models by comprehensively segmenting...
  • Priti Shaw
    Enhance Web Interface for Natural-Language Processing Extracted Interaction Network
    Goal: The goal is to expand on the web interface and the data generation pipeline developed in 2019. Overview: Continuing to the already done work,...
  • Merve Kılıçarslan
    Enhancing PathwayMapper in cBioPortal and PathwayMapper editor
    Pathways are created by selecting certain genes and studies then displayed in the PathwayMapper tab in the cBioPortal. However, not every page in...
  • Mudasir Shaikh
    Generating detailed SBOL representation of genetic logic circuits along with improved designing capability, and Java-Python conversion.
    GeneTech allow users to develop genetic logic circuits only by specifying a Boolean function. The tool first performs Boolean optimisation, followed...
  • Yash Agarwal_
    Implement a comment/discussion system in GraphSpace
    The aim of this project is to implement a real-time comment/discussion and reaction system that will allow users to comment on graphs and discuss...
  • Hemant
    Implementation of SBML-JSON converter and SBML-JSON scheme
    The Systems Biology Markup Language (SBML) is the main language for representation and exchange of computational models in biology. JSON is the main...
  • Sahil Jha
    Improving compmodelmatch.org
    This project intends to make several improvements to compmodelmatch platform which will improve its performance and also add features such as ORCID...
  • Debashish Roy
    Integrating RRPlugins with libRoadRunner
    LibRoadrunner is a high-performance SBML based simulator that uses LLVM to generate very efficient runtime code. This enables LibRoadrunner to...
  • Linhao Meng
    Integration of sequence visualization into SynBioHub
    As a design repository for Synthetic Biology, SynBioHub facilitates the sharing and searching for information, combining data from a variety of...
  • Bhavesh Narra
    LACE-View : A Visualizer for Longitudinal Clonal Trees
    LACEview is a visualization tool for LACE (Longitudnal Analysis of Cancer Evolution) developed by a team at BIMIB. The tool is for R visualization...
  • Saksham Raghuvanshi
    Redevelop Model Bricks code base architecture
    Model Bricks project is an effort focused on describing recurring patterns in biological networks. These patterns are described as small VCell models...
  • Hemil Panchiwala
    Simulation of systems biology models in Java: support for new features
    Systems biology studies the mechanisms underlying complex biological processes as integrated systems of many interacting components. Modeling...
  • Isabel Marleen
    Spreadsheet Plug-in for SynBioHub
    Synthetic Biology is a discipline that connects many disciplines and heterogeneous researchers. To be useful as a tool, a platform such as SynBioHub...
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2020