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 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 page for additional resources and application tips.

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Technologies

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

Topics

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National Resource for Network Biology (NRNB) 2017 Projects

  • Raghav Jajodia
    Adding support for PSIMI-TAB format to the Disease Variant Impact (DV-IMPACT) Database
    The goal of the project would be to add support for PSIMI-TAB format to the admin tools of the DV-IMPACT database and allow the upload and download...
  • Rishabh Sethi
    Cytoscape app for GraphSpace (CyGraphSpace)
    The overall goal of the project is to create a Cytoscape app (CyGraphSpace) for syncing networks from Cytoscape to GraphSpace and vice-versa....
  • Hasan Balcı
    Cytoscape.js Extension for Querying Large Networks
    Traversal-based graph algorithms are good at extracting “subgraphs of interest” when applied to large networks. However, applying known algorithms...
  • Edoardo Galimberti
    cyTRON: a Cytoscape app for the visualization of evolutionary trajectories in cancer progression
    TRONCO is an R package that implements state-of-the-art algorithms for the inference of cancer progressions with the ultimate goal of understanding...
  • Zach Zundel
    Develop a Synthetic Biology Publication Workflow that Leverages the Synthetic Biology Open Language
    A large goal of both the SBOL and synthetic biology communities is to develop a useful and comprehensive workflow from experiment to publication....
  • Takahiro Yamada
    Develop a web service which provides simulation / steady state analysis / parameter estimation with SBML models
    In systems biology, it is very important to formalize the model for biological phenomenon and analyze based on this model basically constructed by...
  • Shaik Asifullah
    Developing a Cluster Computing Framework for Dynamical Modeling
    Integrating the existing Tellurium project with Apache Spark and by which the computations or simulations can be run in parallel. Developing an API...
  • Long Zhang
    Developing a web interface for DoMo-Pred
    Description: The aim of this project is is to develop a web interface for DoMo-Pred which can help to simplify the analysis of protein-protein...
  • bodun
    Extending the IBW Biocompilation Interface with SBOL and SBML Import/Export Capabilities
    The Infobiotics Workbench (IBW) is a synthetic biology design tool with three major functionalities: stochastic simulations, which mimic the...
  • Guodong Xu
    Implement GeneMANIA in Julia for High-performance Computing
    The aim of the project is to Implement GeneMANIA in Julia to optimize netDx for high-performance computing. The current Java-based implementation of...
  • Ivan Bestvina
    Implement Network Quantity Information measure in CentiScaPe #64
    CentiScaPe is a Cytoscape application used to calculate a number of different node centralities of an optionally weighted network, both directed and...
  • Sandeep Mahapatra
    Implementation of a Python Library for GraphSpace RESTful APIs
    In this project, we would be aiming to implement a python library for the GraphSpace RESTful APIs. Implementing such a library will be boon for the...
  • Ilkin Safarli
    Improvements in Tool for Curating Biological Maps in SBGN
    SBGNViz is a Cytoscape.js based library for viewing biological maps in Systems Biology Graphical Notation (SBGN) notation. ChiSE is a library based...
  • Haoran Yu
    Interconversion of the SBML and SBGN Modelling Languages using Semantics of Logic
    Systems biology researchers study the network of molecular interactions within a biological system and publish the deduced models in a diagram...
  • Saurabh Kumar
    libGPML library to read and write GPML files
    libGPML Currently it is required to include the whole PathVisio core module which is much bigger and already contains PathVisio specific...
  • Melvin Mathew
    Notification system for GraphSpace
    GraphSpace is an user-friendly web-based platform that collaborating research groups can utilize for storage, interaction, and network sharing. A...
  • MENGHE ZHANG
    OpenGL-accelerated Renderer for Cytoscape 3
    Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways. It integrates these networks...
  • MWrana
    PiType: A Protein Interaction Prediction Cytoscape App
    PiType is an already existing protein-protein interaction classifying tool created by my mentor. It currently exists as both a web app and a...
  • Bhavesh Narra
    Roadmap to create a WebApp for the Enrichment Map Using Cytoscape and RESTful services
    The Projects goal is to use opencpu and cytoscape.js in order to remove the difficulty for Biologists to tackle with the hassles of using R code...
  • jcbwndsr
    WikiPathways Pathway Presenter
    WikiPathways is an open and collaborative platform for sharing biological pathway information. It features an interactive diagram that aids the user...
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2017