Back to Academy

NRNB Enrolled Students

Rupin Khera - Virginia Tech, Blacksburg, Virginia
PathLinker plugin for PathVisio
Mentored by TM Murali and Martina Summer-Kutmon

NRNB Academy Alumni

2016

Aarya Venkat - University of California San Diego, San Diego, CA
Modeling the Effects of Small Molecule Binders on Pathways in Cytoscape
Mentored by Scooter Morris
Ivan Bestvina - University of Zagreb, Zagreb, Croatia
Random networks for CentiScaPe
Mentored by Gabriele Tosadori

Summer Session 2015

Matthias König - Charité Universitätsmedizin Berlin, Berlin, Germany
Cy3SBML: Make CySBML a Cytoscape 3 app
Mentored by Andreas Dräger and Nicolas Rodriguez
Metin Can Siper - Bilkent University, Ankara, Turkey
Improving Cytoscape.js-based viewer for SBGN process description diagrams with better layout and advanced complexity management operations
Mentored by Uğur Doğrusöz and Onur Sümer
Sakshi Pratap - Birla Institute of Technology and Sciences, Pilani, India
CentiScaPe for multiple networks analysis and graphical output enhancement
Mentored by Giovanni Scardoni
Vijay Dhameliya - Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar, India
Adding PCA to clusterMaker2
Mentored by Scooter Morris

2015

Vijay Dhameliya - Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar, India
Network animation tools
Mentored by Scooter Morris

2013

Chao Zhang - University of Missouri, Columbia, Missouri
NOA and Avalon Cytoscape plugins for visualization and analysis of ontology-annotated networks
Mentored by Alexander Pico

2012

Sravanthi Rani Sinha - KMIT, Hyderabad, India
Develop a stoichiometry plugin for SBGN in PathVisio
Mentored by Martijn van Iersel
Back to GSoC

NRNB GSoC Alumni

We have mentored a total of 121 successfully completed projects by 98 unique students with an overall success rate of 95%.

2017 (20/20 passing students, 100%)

Raghav Jajodia - Indian Institute of Engineering Science and Technology, Shibpur, India
Adding support for PSIMI-TAB format to the Disease Variant Impact (DV-IMPACT) Database
Raghav's GitHub 1 / Raghav's GitHub 2
Raghav's blog
Mentored by Mohamed Helmy
Rishabh Sethi - Indian Institute of Technology, Delhi, India
Cytoscape app for GraphSpace
Rishabh's blog
Mentored by T.M Murali
Hasan Balcı - Bilkent University, Ankara, Turkey
Cytoscape.js Extension for Querying Large Networks
Hasan's blog
Mentored by Ozgun Babur
Edoardo Galimberti - University of Turin, Turin, Italy
cyTRON: a Cytoscape app for the visualization of evolutionary trajectories in cancer progression Zach's report
Mentored by Marco Antoniotti
Zach Zundel - University of Utah, Salt Lake City, US
Develop a Synthetic Biology Publication Workflow that Leverages the Synthetic Biology Open Language
Zach's GitHub 1
Zach's GitHub 2
Zach's blog
Mentored by Neil Wipat
Takahiro Yamada - Keio University, Tokyo, Japan
Develop a web service which provides simulation / steady state analysis / parameter estimation with SBML models
Takahiro's blog
Mentored by Andreas Draeger
Shaik Asifullah - BITS Pilani, Goa, India
Developing a Cluster Computing Framework for Dynamical Modeling
Shaik's blog
Mentored by Kyle Medley
Long Zhang - Chengdu University of Information Technology, Chendu, China
Developing a web interface for DoMo-Pred Long's report"
Mentored by Shobhit Jain
Peter Dun - Stanford University, Palo Alto, US
Extending the IBW Biocompilation Interface with SBOL and SBML Import/Export Capabilities
Peter's blog
Mentored by Harold Fellerman
Guodong Xu -
Implement GeneMANIA in Julia for High-performance Computing
Mentored by Shradda Pai
Ivan Bestvina -
Implement Network Quantity Information measure in CentiScaPe
Mentored by Giovanni Scardoni
Sandeep Mahapatra -
Implementation of a Python Library for GraphSpace RESTful APIs
Mentored by Aditya Bharadwaj
Ilkin Safarli -
Improvements in Tool for Curating Biological Maps in SBGN
Mentored by Alexander Mazein
Haoran Yu -
Interconversion of the SBML and SBGN Modelling Languages using Semantics of Logic
Haoran's blog
Mentored by Nicolas Rodriguez
Saurabh Kumar -
libGPML library to read and write GPML files
Mentored by Martina Summer-Kutmon
Melvin Mathew -
Notification system for GraphSpace
Mentored by Mitch Wagner
Menghe Zhang -
OpenGL-accelerated Renderer for Cytoscape 3
Mentored by Barry Demchak
Michael Wrana -
PiType: A Protein Interaction Prediction Cytoscape App
Mentored by Florian Goebels
Bhavesh Narra -
Roadmap to create a WebApp for the Enrichment Map Using Cytoscape and RESTful services
Mentored by Augustin Luna
Jacob Windsor -
WikiPathways Pathway Presenter
Jacob's blog
Mentored by Egon Willighagen

2016 (15/15 passing students, 100%)

Ashish Tiwari - Arizona State University, Tempe, AZ, USA
Cytoscape command line scripting enhancements
Mentored by Scooter Morris
Julia Gustavsen - University of British Columbia, Vancouver, Canada
Enhance vignettes and plugin use for R package RCy3 for network manipulation using Cytoscape
Julia's blog
Mentored by Augustin Luna
Zhaoyuan Zoe Xi - University of California Los Angeles, Los Angeles, CA, USA
Extending Cytoscape.js: Addition of Clustering Algorithms
Mentored by Mike Kucera
Roman Schulte - Eberhard Karls University, Tübingen, Germany
JSBML Validation System
Roman's blog
Mentored by Andreas Dräger
Mridul Seth - Birla Institute of Technology and Sciences, Pilani, India
Import graphs in multiple formats and Cytoscape files into GraphSpace
Mentored by TM Murali
Metin Can Siper - Bilkent University, Ankara, Turkey
Improving Web Based SBGN Editor SBGNViz.js
Mentored by Ugur Dogrusoz
Tramy Nguyen - University of Utah, Salt Lake City, UT, USA
Interconversion between the systems biology modeling formats SBML and BioPAX
Tramy's blog
Mentored by Mike Hucka
Kaito Ii - Keio University Graduate School of Science and Technology, Tokyo, Japan
Interconvertible Layout program for CellDesigner
Kaito's blog
Mentored by Akira Funahashi
Hovakim Grabski - Russian­ Armenian University, Yerevan, Armenia
Java support for Deviser, a code generation system for SBML libraries
Hovakim's blog
Mentored by Frank T. Bergmann
Ivan Bestvina - University of Zagreb, Zagreb, Croatia
Multithread Centiscape
Mentored by Giovanni Scardoni
Supun Arunoda - University of Moratuwa, Galle, Sri Lanka
Principal Coordinate Analysis and t-Distributed Stochastic Neighbor Embedding in clusterMaker2
Mentored by Scooter Morris
Devesh Khandelwal - University of Delhi, Delhi, India
SBGN-ML and SBML to Escher Converter
Devesh's blog
Mentored by Zachary A. King
William Miles - McMaster University, Hamilton, Canada
The Online Resource for Interface Based Interaction Networks (TOR-IBIN) Web Interface
Mentored by Mohamed Helmy
Joseph Stahl - Vanderbuilt University, Nasville, TN, USA
Tutorials for Cytoscape.js
Mentored by Max Franz
Istemi Bahceci - Bilkent University, Ankara, Turkey
Visualizing genomic alterations in TCGA cancer pathways in cBioPortal
Mentored by Ugur Dogrusoz

2015 (3/4 passing students, 75%), 2015 NRNB Academy Summer Session

2014 (17/18 passing students, 94%)

Abhiraj Tomar - University of Southern California, Los Angeles, CA, USA
Implementation of new clustering techniques into Cytoscape
Mentored by Scooter Morris
Adam Shaw - University of Chicago, Chicago, IL, USA
Hierarchical Models in Segway
Mentored by Michael Hoffman
Alex Crits-Christoph - Johns Hopkins University, Baltimore, MD, USA
Developing An Interface For The Cancer Network Altering Variant Database
Mentored by Mohamed Helmy
Arman Aksoy - Memorial Sloan-Kettering Cancer Center, New York, NY, USA
Pathway Database Converters for the Expansion of Pathway Commons
Mentored by Augustin Luna
Truhin Alexandr - Technical University of Moldova, Chisinau, Moldova
Pathvisiojs Diff Viewer
Mentored by Anders Riutta
Shaik Faizaan - Birla Institute of Technology and Sciences, Pilani, India
Porting Interference App to Cytoscape 3
Mentored by Giovanni Scardoni
Rohan Saxena - Birla Institute of Technology and Sciences, Pilani, India
PathVisio Plugin to Load Additional Information about Data Nodes
Mentored by Martina Kutmon
Ankit Agarwal - Manipal University, Manipal, India
Virtual Cell iPhone App Enhancements
Mentored by Jim Schaff
Gerardo Huck - National University of Rosario, Rosario, Argentina
Graph Analysis Algorithms for Cytoscape.js
Mentored by Max Franz
Jonathan Melius - University of Maastricht, Maastricht, The Netherlands
Connect PathVisio and WikiPathways to Expression Atlas
Mentored by Lars Eijssen
Kirtan Dave - Sardar Patel University, Vallabh Vidyanagar, India
New Features for Interference App
Mentored by Cristian Munteanu
Lilit Nersisyan - National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
PSFC: a Cytoscape app for calculating pathway signal flows
Mentored by Graham Johnson
Jimmy Morzaria - Birla Institute of Technology and Sciences, Pilani, India
Network Analysis Enhancements
Mentored by Jason Montojo
Niranjan Padmanabhan - McGill University, Montreal, Canada
ADAM Variation Services and Visualizations for Cytoscape 3 Variation App
Mentored by Michael Heuer
Sakshi Pratap - Birla Institute of Technology and Sciences, Pilani, India
Porting Pesca App to Cytoscape 3 with new features
Mentored by Giovanni Scardoni
Srikanth Bezawada - Birla Institute of Technology and Sciences, Pilani, India
Implementing TieDIE algorithm as a Cytoscape App
Mentored by Evan Paull

2013 (14/15 passing students, 94%)

Abhiraj Tomar - Birla Institute of Technology and Sciences, Pilani, India
Implementation of Fuzzy Clusters in Cytoscape
Mentored by Scooter Morris
Alvin Leung - McGill University, Montreal, Canada
Implementing a Cytoscape 3.0 app for the HyperModules algorithm
Mentored by Gary Bader
Ankit Agarwal - Manipal University, Manipal, India
iPhone application for viewing of public/private results in the Virtual Cell
Mentored by Jim Schaff
Christ Leemans - University of Maastricht, Maastricht, The Netherlands
Automated pathway-creation plugin for PathVisio
Mentored by Andra Waagmeester
Diego Magagna - Verona University, Veneto, Italy
Multiplication of nodes and directed graphs in Cytoscape 3
Mentored by Giovanni Scardoni
Gerardo Huck - National University of Rosario, Rosario, Argentina
Compound Graph Layout Algorithm for Cytoscape.js
Mentored by Max Franz
Istemi Bahceci - Bilkent University, Ankara, Turkey
Specialized Layout Algorithm for SBGN Process Description Diagrams
Mentored by Ugur Dogrusoz
Jimmy Morzaria - Birla Institute of Technology and Sciences, Pilani, India
Visualization of Dynamic Graphs in Cytoscape
Mentored by Jason Montojo
Li Zhang - Jilin University, Changchun, China
Identifier Mapping App for Cytoscape 3.0
Mentored by Chao Zhang
Ritisha Laungani - Birla Institute of Technology and Sciences, Pilani, India
Modeling and Visualizing Cell Signaling Networks with SigViz
Mentored by Graham Johnson
Shaik Faizaan - Birla Institute of Technology and Sciences, Pilani, India
CentiScaPe Development and addition of extra Centrality parameter called Eigenvector Centrality
Mentored by Giovanni Scardoni
Sravanthi Sinha - Keshav Memorial Institute of Technology, Hyderabad, India
WikiPathways client plugin for PathVisio
Mentored by Martina Kutmon
Sri Harsha - Keshav Memorial Institute of Technology, Hyderabad, India
SBML Importer Plugin for PathVisio
Mentored by Anwesha Dutta
Truhin Alexandr - Technical University of Moldova, Chisinau, Moldova
Bird's eye view pan control for Cytoscape.js
Mentored by Christian Lopes

2012 (16/16 passing students, 100%)

Anwesha Dutta - University of Maastricht, Maastricht, The Netherlands
Extend PathVisio with a plugin to create , modify and visualize data on biological pathways from scripting languages
Mentored by Martina Kutmon
Chao Zhang - University of Missouri, Columbia, Missouri
Ontology-based Network Visualization and Analysis
Mentored by Alexander Pico
David Shih - University of Toronto, Toronto, Canada
Porting HOPACH cluster algorithm into clusterMaker
Mentored by Scooter Morris
Dazhi Jiao - Indiana University, Bloomington, IN, USA
Cytoscape Plugin for importing cancer genomic data and drug-target interaction data from cBio Cancer Genomic Portal
Mentored by Arman Aksoy
Istemi Bahceci - Bilkent University, Ankara, Turkey
SBGN-Complaint Views for Cancer Genomics Networks
Mentored by Ugur Dogrusoz
Jake Fried - University of Maryland, College Park, MD, USA
Understanding Complex Pathways using User Data and Web Services in PathVisio
Mentored by Augustin Luna
Khushi Chachcha - University of British Columbia, Vancouver Canada
GeneMANIA plugin for MedSavant
Mentored by Marc Fiume
Michael Kirby - University of California, San Diego, CA, USA
A Direct Interface Between R and Cytoscape
Mentored by Mike Smoot
Neil Dhruva - Birla Institute of Technology and Science, Pilani, India
Data summary of tables in Cytoscape
Mentored by Samad Lotia
Praveen Kumar - Jawaharlal Nehru Technological University, Hyderabad, India
Pathway Comparison in PathVisio
Mentored by Martina Kutmon
Rianne Fijten - University of Maastricht, Maastricht, The Netherlands
Plugin for metabolite information in Pathvisio
Mentored by Egon Willighagen
Ritisha Laungani - Birla Institute of Technology and Science, Pilani, India
Interactive path explorer through networks and biological pathways for Cytoscape
Mentored by Alexander Pico
Sabina Sara Pfister - University of Zurich, Zurich, Switzerland
Loading and visualization of dynamical networks in Cytoscape 3.0
Mentored by John Brown
Sinan Sonlu - Bilkent University, Ankara, Turkey
Layout Algorithms for New Cytoscape Web
Mentored by Ugur Dogrusoz
Yigang Zhou - Wuhan University, Wuhan, China
Visualizing Semantic Data Landscapes with Cytoscape 3.0
Mentored by Andra Waagmeester
Yue Dong - University of Toronto, Toronto, Canada
Cytoscape App Manager, Cytoscape Web WebGL Renderer and Layouts, Presentation API Testing
Mentored by Jason Montojo

2011 (8/10 passing students, 80%)

Chao Zhang - University of Missouri, Columbia, MO, USA
GOLayout: Network partitioning and layout driven by GO ontology
Mentored by Alexander Pico
Martina Kutmon - University of Maastricht, Maastricht, The Netherlands
New PathVisio Plug-in Manager
Mentored by Martijn van Iersel
Marek Zaluski - Concordia University, Montreal, Canada
HTML5 prototype for Cytoscape Web
Mentored by Christian Lopes
Gerardo Huck - National University of Rosario, Rosario, Argentina
Connecting Cytoscape with igraph
Mentored by Gang Su
Avinash Thummala - IIIT-H, Hyderabad, India
A Cytoscape build with a fused (Annotation + Basic) editor based on an improved CyNetworkView with Neo4j interoperability
Mentored by Scooter Morris
Andrew Brook - University of Toronto, Toronto, Canada
Integrate Pathway Visualization and Analysis into Savant
Mentored by Marc Fiume
Yue Dong - University of Toronto, Toronto, Canada
Cytoscape Web - HTML5 Prototype
Mentored by Jason Montojo
Kumar Chandan - Keshav Memorial Institute of Technology (KMIT), Hyderabad, India
Real-time Validation Framework for Pathvisio
Mentored by Augustin Luna

2010 (10/10 passing students, 100%)

Leontius Pradhana - National University of Singapore, Singapore, Singapore
Reactome-Wikipathways Round-trip Format Converter
Mentored by Guanming Wu
Gerardo Huck - National University of Rosario, Rosario, Argentina
Improving Cytoscape's Labels Experience
Mentored by Mike Smoot
Kozo Nishida - Nara Institute of Science and Technology, Nara, Japan
KEGG global map browser and its integration to Processing visualizer
Mentored by Keiichiro Ono
Bing Liu - National University of Singapore, Singapore, Singapore
Improve the PathVisio User Interface
Mentored by Kristina Hanspers
Dazhi Jiao - Indiana University, Bloomington, IN, USA
Expression Data Reader plugin for Cytoscape
Mentored by Alexander Pico
Anurag Sharma - KIIT University, Bhubaneswar, Bhubaneswar, India
Perform Microarray Summarization and Alternative Splicing Analyses By Coupling the Programs AltAnalyze and GenMAPP-CS
Mentored by Nathan Salomonis
Tomithy Too - National University of Singapore, Singapore, Singapore
Proposal for the Implementation of Edge-Weighted Force Directed layout for Cytoscapeweb
Mentored by Christian Lopes
Layla Oesper - University of Wisconsin, Madison, WI, USA
Using NLP Techniques to Create a Semantic Network Summary for Cytoscape
Mentored by Ruth Isserlin
Chetan Bansal - Birla Institute of Technology and Science Pilani, Goa, Hyderabad, India
Exploring relations between pathways on WikiPathways
Mentored by Thomas Kelder
Avinash Thummala - IIIT-H, Hyderabad, India
Creating a CyAnnotator and improving CyAnimator
Mentored by Scooter Morris

2009 (9/10 passing students, 90%)

Gerardo Huck - National University of Rosario, Rosario, Argentina
Cytoscape GPU Assisted Graph Layout Plugin
Mentored by Daniel Abel
Jianjiong Gao - University of Missouri, Columbia, MO, USA
ID mapper API and plugin for Cytoscape
Mentored by David States
Stephen Federowicz - UCSC, Santa Cruz, CA, USA
CyAnimator: A general purpose animation tool for Cytoscape
Mentored by Scooter Morris
Adem Bilican - University of Maastricht, Maastricht, The Netherlands
Biopax plugin(import, layout, export) for PathVisio
Mentored by Martijn van Iersel
Helen Xuemin Liu - Iowa State University, Ames, Kansas City, MO, USA
Superpathways in Cytoscape
Mentored by Thomas Kelder
Chinmoy Bhatiya - Denison University, Granville, OH, USA
Phylogenetic tree plugin for Cytoscape
Mentored by Pen-Liang Wang
Chetan Bansal - Birla Institute of Technology and Science Pilani, Goa, Hyderabad, India
Ontologies for Wiki Pathways
Mentored by Alexander Pico
Kozo Nishida - Nara Institute of Science and Technology, Nara, Japan
Processing-Based New Visualizer for Cytoscape 3
Mentored by Keiichiro Ono
Vundavalli Srinivasarao - IIIT-H, Hyderabad, India
Integrated data mining in Cytoscape 3.0
Mentored by Maital Ashkenazi

2008 (8/9 passing students, 89%)

Patrick McSweeney - Syracuse University, Syracuse, USA
Random Network Plugin
Mentored by Maital Ashkenazi
Victoria Mui - University of Toronto, Toronto, Canada
Automatic (Smart) Node and Edge Label Layout
Mentored by Greg Wilson
Gang Su - University of Michigan, Ann Arbor, MI, USA
Normalizing Visualization with Hierarchical Community Structure
Mentored by Allan Kuchinsky
Dazhi Jiao - Indiana University, Bloomington, IN, USA
Integration of Cheminformatics Tools in Cytoscape
Mentored by Scooter Morris
Jianjiong Gao - University of Missouri, Columbia, MO, USA
Advanced network merge for Cytoscape
Mentored by Keiichiro Ono
Bulent Arman Aksoy - Bogazici University, Istanbul, Turkey
Advanced network merge for Cytoscape
Mentored by Thomas Kelder
Stephen Federowicz - UCSC, Santa Cruz, CA, USA
Implementing Boolean Logic into the Display of Visual attributes
Mentored by Alexander Pico
Daniel Abel - Eotvos University, ELTE, Budapest, Hungary
Implement long-standing cytoscape wishlist features in cytoscape core
Mentored by Mike Smoot

2007 (4/4 passing students, 100%)

Nikolic Aleksandar - University of Nis, Leskovac, Serbia
Graph layout library for Cytoscape
Mentored by Mike Smoot
Maital Ashkenazi - The Hebrew University, Jerusalum, Israel
Enhanced search strategy in Cytoscape
Mentored by David States
Thomas Kelder - University of Maastricht, Maastricht, The Netherlands
Pathway editor for wikipathways
Mentored by Kristina Hanspers
Martijn van Iersel - University of Maastricht, Maastricht, The Netherlands
Visual history of pathway modifications
Mentored by Alexander Pico
Back to GSoC