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
  • c++
  • web

Topics

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National Resource for Network Biology (NRNB) 2019 Projects

  • Sarthak Srivastava
    App Store for Cytoscape Apps
    I am interested in the project “Appstore for the Cytoscape App” with Alex Pico, Barry Demchak and Scooter Morris as its mentor. My goals for the...
  • Manas Awasthi
    BridgeDb Major Release
    BridgeDb is a platform used for identifier mapping in WikiPathways and PathVisio with support for various languages like as a Cytoscape plugin, as an...
  • Perman Atayev
    CiSE layout as a Cytoscape.js extension and an automated layout web service for popular Cytoscape.js layout extensions
    Automated layout web service with an integrated converter, to change the format of the data, would be of great use for people who want to quickly and...
  • Kaustubh Trivedi
    Extending ModelPolisher to a universal model annotation tool
    ModelPolisher is a model annotation tool for the BiGG Models Knowledgebase. Annotations enhance the reusability and interoperability of biological...
  • Daniyal Jahan
    GraphSpace: Diffs for graphs
    The goal of this project ‘Diff for Graphs’ is to implement a graph comparison functionality which will allow users to compare two or more graphs that...
  • Ayush Ranjan Lohani
    Implement a machine-readable graph legend interface
    The overall goal of this project is to implement a machine-readable graph legend interface and extend the API to add, modify and remove legend data...
  • Debashish Roy
    Integrating RRPlugins with libRoadRunner and devloping Differential Evolution optimizer plugin
    LibRoadrunner is a high performance SBML based simulator that uses LLVM to generate very efficient runtime code. This enables LibRoadrunner to...
  • Nikhil Ghodke
    New Build System for InSilico
    InSilico is an extensible editor which can be used for manipulating and analyzing many different file types, SBML files in particular. The current...
  • Robin Simonot
    Simulator for Systems Biology
    Develop a simulator which will support all the features of SBML core specification Implement a code so that the simulator can pass testcases which...
  • Bhavye Jain
    Validation of spatial systems biology models in Java
    The spatial extension for SBML provides support for describing processes that involve a spatial component. This project seeks to implement validation...
  • Rohit R. Chattopadhyay
    Web Interface for NLP Extracted Interaction Network
    An application for users to access biological data extracted from biomedical literature. Project Mentor Augustin Luna Objectives Easy search...
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2019