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 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
  • html
  • c/c++

Topics

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National Resource for Network Biology (NRNB) 2018 Projects

  • Sarthak Srivastava
    App Store for Cytoscape Apps
    The project is “Appstore for the CytoScape Apps” with Alex Pico, Barry Demchak and Scooter Morris as its mentor. The goals for the summer will be to...
  • Lucrezia Patruno
    Develop cyTRON/JS: a backend and a cytoscape.js visualizer for cancer progression models
    This project aims at developing a tool which should provide an interactive visualization of the cancer progression models produced by the R library...
  • Daniyal
    GraphSpace: Git for graphs
    GraphSpace is a web-based platform where collaborating research groups can use a user-friendly interface to create, interact and share networks....
  • Vineeth Chelur
    Implement SBML Array Support in libRoadRunner
    LibRoadrunner is a high-performance SBML based simulator for Systems and Synthetic Biology that uses LLVM to generate very efficient runtime code....
  • Ahmet Çandıroğlu
    Improvements for Newt, a Cytoscape.js based SBGN editor
    Newt is a free, web-based, open source viewer and editor for pathways in Systems Biological Graphical Notation (SBGN). It is written with a series of...
  • Prem Prakash Singh
    Integrating CAD and CAM tools for automating a synthetic biology workflow
    Integrated Build Software Optimisation Tools (BOOST) with SBOLDesigner. SBOLDesigner is a CAD tool for creating and manipulating the sequences of...
  • Kaan Sancak
    PathwayMapper Improvements and Integration into cBioPortal
    While the network visualization module in cBioPortal is a powerful exploration tool, most biologists are more comfortable with the kind of...
  • Sunwoo Kang
    Rendering Complex Genetic Design with DNAplotlib for a Beautiful Visualization of Genetic Circuit
    Visualizing genetic circuits is essential in the field of synthetic biology. These genetic designs often involve complex representation of modular...
  • Shalin
    Simulating systems biology models in Java
    Computational models of biological systems play an important role in advancing science as they give insights about the biology without the need for...
  • Dara Akdag
    Upgrading Ontology Tagging at WikiPathways
    Ontologies are an integral part of our scientific progress. The ability to share common definitions is crucial to answering questions, thus, an...
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2018