National Resource for Network Biology (NRNB)

Developing open source software to enable network-based biomedical discovery

Technologies
python, javascript, c/c++, java, html
Topics
data visualization, web applications, biology, network analysis, data modeling
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.

2018 Program

Successful Projects

Contributor
Lucrezia Patruno
Mentor
Daniele Ramazzotti, Marco Antoniotti
Organization
National Resource for Network Biology (NRNB)
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...
Contributor
Vineeth Chelur
Mentor
Chris Myers, Herbert Sauro, Leandro Watanabe
Organization
National Resource for Network Biology (NRNB)
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....
Contributor
Prem Prakash Singh
Mentor
Chris Myers, Michael Zhang, Ernst Oberortner
Organization
National Resource for Network Biology (NRNB)
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...
Contributor
Ahmet Çandıroğlu
Mentor
Ugur Dogrusoz, Alexander Mazein
Organization
National Resource for Network Biology (NRNB)
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...
Contributor
Kaan Sancak
Mentor
Ugur Dogrusoz, Onur, JJ Gao
Organization
National Resource for Network Biology (NRNB)
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...
Contributor
Sarthak Srivastava
Mentor
Scooter Morris, Alexander Pico
Organization
National Resource for Network Biology (NRNB)
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...
Contributor
Shalin
Mentor
Hannes Planatscher, Nicolas Rodriguez, Matthias König, Andreas Dräger
Organization
National Resource for Network Biology (NRNB)
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...
Contributor
Daniyal
Mentor
Aditya Bharadwaj, Jing Cui
Organization
National Resource for Network Biology (NRNB)
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....
Contributor
Dara Akdag
Mentor
Martina Summer-Kutmon, Alexander Pico
Organization
National Resource for Network Biology (NRNB)
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...
Contributor
Sunwoo Kang
Mentor
Bryan Bartley, Thomas Gorochowski
Organization
National Resource for Network Biology (NRNB)
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...