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NRNB GSoC Alumni

We have mentored a total of 197 successfully completed projects by 165 unique students with an overall success rate of 96%

2024 (11/11 passing students, 100%)

Tushar Choudhary - BITS Pilani, Pilani, India

Cytoscape layout plugin to support Cytoscape.js layouts
Mentored by Hasan Balci

Umut Utku Erşahince - Bilkent University, Ankara, Turkey

Machine Learning Support for Constructing Newt SBGN Maps
Mentored by Uğur Doğrusöz

Johan Guillen - Brightmont Academy, Seattle, USA

Integration of complexity score functions into the iGEM DNA kit distribution workflow
Mentored by Gonzalo Vidal

Favour James - Obafemi Awolowo University, Ife, Nigeria

Large Language Model-based creation of knowledge graph from a publication
Mentored by Dexter Pratt

Vishnu Madhav - Institute of Bioinformatics and Applied Biotechnology, Bangalore, India

Integration of GRN inference algorithms using single cell multi-omics data to BEELINE
Mentored by Yiqi Su

Luca Milazzo - Università degli studi di Milano-Bicocca, Milan, Italy

COBRAxy: COBRA and MaREA4Galaxy
Mentored by Chiara Damiani

Nada Mohamed - Università degli studi di Milano-Bicocca, Milan, Italy

ASCETIC 2.0
Mentored by Daniele Ramazzotti

Deep Poharkar - Pimpri Chinchwad College Of Engineering, Pune, India

Implement AWS DevOps Pipeline for Image Deployment for Graphspace
Mentored by Mahesh Kasbe

Faizal Rahman - Jawaharlal Nehru University, New Dehli, India

Using Foundation Model: scGPT for Gene Regulatory Network Inference
Mentored by Nure Tasnina

Aditya Saini - ABES Engineering College, Ghaziabad, India

GPML support in Newt
Mentored by Hasan Balci

Mohamed Soudy - University of Luxembourg, Luxembourg, Belgium

Improvement Of openPIP (Data upload and Visualization)
Mentored by Mohamed Helmy

2023 (8/8 passing students, 100%)

Siddharth Chaudhary - The LNM Institute Of Information Technology, India

Implement a R shiny module for Network Analysis in CellMinerCDB
Mentored by Augustin Luna

Jigyasa Gupta - Dayananda Sagar College of Engineering, Bangalore, India

Supporting Pathway Commons and ssGSEA in clusterProfiler
Mentored by Guangchuang Yu

Favour James - Obafemi Awolowo University, Ife, Nigeria

Generate Example Dataset for PyTorch Geometric Based on Pathway Commons and Prototype
Mentored by Yoshitaka Inoue

Mahesh Kasbe - Bhavans College, Mumbai India

Setting up the CI/CD Pipeline using Github Actions on GraphSpace
Mentored by Yash Agrawal

Ermis Delopoulos - Katholieke Universiteit Leuven, Leuven, Belgium

Development of a Cytoscape App for microbe-microbe association networks
Mentored by Scooter Morris

Akash Mondal - The LNM Institute Of Information Technology, India

Automate Cytoscape.js release process using GitHub Actions
Mentored by Max Franz

Phuc Nguyen - University of Cincinnati, Cincinnati, OH, USA

Convert CellBox code from Tensorflow to Pytorch
Mentored by Bo Yuan

Kartik Kumar Pawar - Jawaharlal Nehru University, New Dehli, India

Develop new features for Cytoscape App - cyPlot
Mentored by Yihang Xin

2022 (8/10 passing students, 80%)

Selbi Ereshova - Bilkent University, Ankara, Turkey

SBML-MINERVA support in Newt
Mentored by Alexander Mazein

Yoshitaka Inoue - University of Minnesota, MN, USA

Create a Pipeline from data extraction to execution of GNN based Drug Response Prediction
Mentored by Augustin Luna

Sara Jovanovska - Utrecht University, Utrecht, The Netherlands

NetBoxR Updates
Mentored by Eric Liu

Mohit Makwana - Birla Institute of Technology and Science, Mumbai, India

Conversion between GenBank and SBOL3
Mentored by Tom Mitchell

Akash Mondal - The LNM Institute Of Information Technology, Jaipur, India

Updates to the Enrichment Table App
Mentored by Alex Pico

Aniket Ranjan - Indian Institute of Technology, Kharagpur, India

Adding visualization of protein-complex interaction to OpenPIP
Mentored by Gary Bader

Fizza Rubab - Habib University, Karachi, Pakistan

Cloud-COPASI
Mentored by Hasan Baig

Aditya Singhal - Lakehead University, Thunder Bay, Canada

Create Jupyter Notebooks showcasing COMBINE Standards
Mentored by Matthias König

2021 (13/14 passing students, 93%)

Javed Ali - Indian Institute of Technology Kharagpur, Dehli, India

Adding analysis report and Direct import from GEO databases to ABioTrans Plus
Mentored by Mohamed Helmy

Can Alpay - Bilkent University, Ankara, Turkey

PD to AF conversion facility in Newt
Mentored by Alexander Mazein

Pranav Ballaney - Birla Institute of Technology and Science, Pilani, India

SBML Simulator in Rust
Pranav's blog
Mentored by Akito Tabira

Sankha Das - Birla Institute of Technology and Science, Pilani, India

SBML4Humans - Interactive SBML Report for Humans
Sankha's blog
Mentored by Matthias König

Indraneel Ghosh - Birla Institute of Technology and Science, Pilani, India

Simple Enrichment Tool for Analysis
Mentored by Alex Pico

Siras Hakobyan - Institute of Molecular Biology NAS RA, Yerevan, Armenia

TumorComparer, updated version
Mentored by Augustin Luna

Noah Liguori-Bills - The University of Connecticut, CT, USA

Expand ModelBricks.org and VCell API
Mentored by Michael Blinov

Nikita Mahoviya - National Institute of Technology Hamirpur, Lucknow, India

Develop GUI for ImageJ groovy script calling VCell API
Nikita's blog
Mentored by Anne Cowan

Aniket Ranjan - Indian Institute of Technology Kharagpur, Kharagpur, India

Enhancing the admin panel of openPIP
Mentored by Gary Bader

Pritam Saha - Jadavpur University, Kolkata, India

Develop a Cytoscape App for the Casual Path Algorithm
Mentored by Ozgun Babur

Mohmed Soudy - Ain Shams University, Cairo, Egypt

Adding Multi-omics data support to ABioTrans Plus
Mohmed's blog
Mentored by Thuy Tien Bui

Maija Utriainen - Maastricht University, Maastricht, The Netherlands

Implementing multiple clustering algorithms and dimensionality reduction techniques on clusterMaker2
Mentored by Scooter Morris

Pankaj Yadav - Indian Institute of Technology, Varanasi, India

Local DB support for SBGN maps in Newt
Mentored by Uğur Doğrusöz

2020 (15/15 passing students, 100%)

Rahul Agrawal - Indian Institute of Technology, Kharagpur, India

Adding Network Analysis and Visualisation Features to ABioTrans
Mentored by Mohamed Helmy

Yash Agrawal - Indian Institute of Technology, Guwahati, India

Implement a comment/discussion system in GraphSpace Yash's blog
Mentored by Daniyal Jahan

Medha Bhattacharya - Indira Gandhi Delhi Technical University for Women, New Delhi, India

Development of a system that generates spatial SBML models using deep learning
Medha's blog
Mentored by Akira Funahashi

Sahil Jha - Amity university, New Delhi, India

Improving compmodelmatch.org Sahil's blog
Mentored by Michael Blinov

Merve Kılıçarslan - Bilkent University, Ankara, Turkey

Enhancing PathwayMapper in cBioPortal and PathwayMapper editor Merve's blog
Mentored by Uğur Doğrusöz

Alice Meng - Zhejiang University, Hangzhou, China

Integration of sequence visualization into SynBioHub
Alice's blog
Mentored by Geoff Baldwin

Bhavesh Narra - Birla Institute of Technology and Sciences, Pilani, India

LACE-View : A Visualizer for Longitudinal Clonal Trees
Mentored by Marco Antoniotti

Hemil Panchiwala - Indian Institute of Technology Roorkee, Roorkee, India

Simulation of systems biology models in Java: support for new features Hemil's blog
Mentored by Andreas Dräger

Isabel Pötzsch - University of Cambridge, Wiesbaden, Germany

Spreadsheet Plug-in for SynBioHub Isabel's blog
Mentored by Jet Mante

Saksham Raghuvanshi - JSS Academy of Technical Education, Noida, India

Redevelop Model Bricks code base architecture
Mentored by Frank Morgan

Debashish Roy - Jabalpur Engineering College, Jabalpur, India

Developing an Optimization Library for libRoadRunner Debashish's blog
Mentored by Herbert Sauro

Mudasir Shaikh - Habib University, Karachi, Pakistan

Generating detailed SBOL representation of genetic logic circuits along with improved designing capability, and SBML export in GeneTech Mudasir's blog
Mentored by Hasan Baig

Priti Shaw - Jadavpur University, Kolkata, India

Enhance Web Interface for Natural-Language Processing Extracted Interaction Network
Mentored by Augustin Luna

Maija Utriainen - Maastricht University, Maastricht, The Netherlands

Implementing R-MCL, ML-MCL, Louvain and Leiden clustering algorithms to Cytoscape app ClusterMaker2
Mentored by Scooter Morris

Hemant Yadav - Indian Institute of Technology Roorkee, Roorkee, India

Implementation of SBML-JSON converter and SBML-JSON scheme Hemant's blog
Mentored by Matthias König

2019 (11/11 passing students, 100%)

Perman Atayev - Bilkent university, Ankara, Turkey

CiSE layout as a Cytoscape.js extension and an automated layout web service for popular Cytoscape.js layout extensions
Mentored by Uğur Doğrusöz

Manas Awasthi - Cluster Innovation Centre, University of Delhi, New Delhi, India

BridgeDb Major Release
Mentored by Egon Willighagen

Rohit R. Chattopadhyay - Jadavpur University, Kolkata, India

Web Interface for NLP Extracted Interaction Network
Rohit's blog
Mentored by Augustin Luna

Nikhil Ghodke - Vishwakarma Institute of Technology, Pune, India

New Build System for Insilico
Nikhil's blog
Mentored by Roman Schulte

Daniyal Jahan - Technische Universität Berlin, Berlin, Germany

GraphSpace: Diff for Graphs
Mentored by T.M. Murali

Bhavye Jain - Indian Institute of Technology, Roorkee, India

Validation of spatial systems biology models in Java
Bhavye's blog
Mentored by Nicolas Rodiguez

Ayush Ranjan Lohani - Indian Institute of Engineering Science And Technology, Shibpur, Kolkata, India

Implement a machine-readable graph legend interface
Mentored by Aditya Bharadwaj

Debashish Roy - Jabalpur Engineering College, Katni, India

Integrating RRPlugins with libRoadRunner and devloping Differential Evolution optimizer plugin
Debashish's blog
Mentored by Herbert Sauro

Robin Simonot - Université de Nantes, Paris, France

Simulator for Systems Biology
Mentored by Akira Funahashi

Sarthak Srivastava - Birla Institute of Technology and Sciences, Pilani, India

App Store for Cytoscape Apps
Mentored by Alex Pico

Kaustubh Trivedi - Indian Institute of Technology - Roorkee, India

Extending ModelPolisher to a universal model annotation tool
Mentored by Matthias König

2018 (10/10 passing students, 100%)

Dara Akdag - Maastricht University, Maastricht, The Netherlands

Upgrading ontology tagging at WikiPathways
Mentored by Martina Kutmon

Vineeth Chelur - International Institute of Information Technology(IIIT), Hyderabad, India

Implement SBML array support in libRoadRunner
Vineeth's blog
Mentored by Herbert Sauro

Daniyal Jahan - Technical University of Berlin, Berlin, Germany

Git for Graphs
Daniyal's blog
Mentored by Aditya Bharadwaj

Sunwoo Kang - Stanford University of Berlin, Stanford, CA, USA

Rendering complex genetic designs with dnaplotlib for a beautiful visualization of genetic circuits
Sunwoo's blog
Mentored by Bryan Bartley

Lucrezia Patruno - University of Milano-Bicocca, Milan, Italy

cyTRON/JS: a backend and a cytoscape.js visualizer for cancer progression models
Mentored by Marco Antoniotti

Kaan Sancak - Bilkent University, Ankara, Turkey

PathwayMapper improvements and integration into cBioPortal
Kaan's blog
Mentored by Onur Sumer

Shalin Shah - Duke University, Durham, NC, USA

Simulating systems biology models in Java
Shalin's blog
Mentored by Andreas Drager

Prem Prakash Singh - Birla Institute of Technology and Science, Pilani, India

Integrating CAD and CAM tools for automating a synthetic biology workflow
Prem's GitHub 1 / Prem's GitHub 2 / Prem's blog
Mentored by Ernst Oberortner

Sarthak Srivastava - Birla Institute of Technology and Sciences, New Delhi, India

App Store for Cytoscape Apps
Mentored by Alex Pico

Ahmet Çandıroğlu - Bilkent University, Ankara, Turkey

Improvements for Newt, a Cytoscape.js based SBGN editor
Ahmet's blog
Mentored by Uğur Doğrusöz

2017 (20/20 passing students, 100%)

Shaik Asifullah - BITS Pilani, Goa, India

Developing a Cluster Computing Framework for Dynamical Modeling
Shaik's blog
Mentored by Kyle Medley

Hasan Balcı - Bilkent University, Ankara, Turkey

Cytoscape.js Extension for Querying Large Networks
Hasan's blog
Mentored by Ozgun Babur

Ivan Bestvina - University of Zagreb, Zagreb, Croatia

Implement Network Quantity Information measure in CentiScaPe
Mentored by Giovanni Scardoni

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

Edoardo Galimberti - University of Turin, Turin, Italy

cyTRON: a Cytoscape app for the visualization of evolutionary trajectories in cancer progression
Edoardo's report
Mentored by Marco Antoniotti

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

Saurabh Kumar - Indian Institute of Technology Delhi, New Dehli, India

libGPML library to read and write GPML files
Mentored by Martina Summer-Kutmon

Sandeep Mahapatra - College of Engineering and Technology, Bhubaneswar, India

Implementation of a Python Library for GraphSpace RESTful APIs
Sandeep's blog
Mentored by Aditya Bharadwaj

Melvin Mathew - University of Southern California, Los Angeles, CA, USA

Notification system for GraphSpace
Melvin's blog
Mentored by Mitch Wagner

Bhavesh Narra - BITS Pilani, Pilani, India

Roadmap to create a WebApp for the Enrichment Map Using Cytoscape and RESTful services
Mentored by Augustin Luna

Ilkin Safarli - Bilkent University, Ankara, Turkey

Improvements in Tool for Curating Biological Maps in SBGN
Mentored by Alexander Mazein

Rishabh Sethi - Indian Institute of Technology, Delhi, India

Cytoscape app for GraphSpace
Rishabh's blog
Mentored by T.M Murali

Jacob Windsor - Maastricht University, Maastricht, The Netherlands

WikiPathways Pathway Presenter
Jacob's blog
Mentored by Egon Willighagen

Michael Wrana - Royal St. George’s College, Toronto, Canada

PiType: A Protein Interaction Prediction Cytoscape App
Mentored by Florian Goebels

Guodong Xu - Wuhan University of Technology, Wuhan, China

Implement GeneMANIA in Julia for High-performance Computing
Mentored by Shradda Pai

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 Kaito Li

Haoran Yu - University of British Columbia, Vancouver, Canada

Interconversion of the SBML and SBGN Modelling Languages using Semantics of Logic
Haoran's blog
Mentored by Nicolas Rodriguez

Long Zhang - Chengdu University of Information Technology, Chendu, China

Developing a web interface for DoMo-Pred
Long's report
Mentored by Shobhit Jain

Menghe Zhang - University of California San Diego, San Diego, CA, USA

OpenGL-accelerated Renderer for Cytoscape 3
Menghe's blog
Mentored by Barry Demchak

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

2016 (15/15 passing students, 100%)

Supun Arunoda - University of Moratuwa, Galle, Sri Lanka

Principal Coordinate Analysis and t-Distributed Stochastic Neighbor Embedding in clusterMaker2
Mentored by Scooter Morris

Istemi Bahceci - Bilkent University, Ankara, Turkey

Visualizing genomic alterations in TCGA cancer pathways in cBioPortal
Mentored by Uğur Doğrusöz

Ivan Bestvina - University of Zagreb, Zagreb, Croatia

Multithread Centiscape
Mentored by Giovanni Scardoni

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

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

Kaito Ii - Keio University Graduate School of Science and Technology, Tokyo, Japan

Interconvertible Layout program for CellDesigner
Kaito's blog
Mentored by Akira Funahashi

Devesh Khandelwal - University of Delhi, Delhi, India

SBGN-ML and SBML to Escher Converter
Devesh's blog
Mentored by Zachary A. King

Miles Mee - McMaster University, Hamilton, Canada

The Online Resource for Interface Based Interaction Networks (TOR-IBIN) Web Interface
Mentored by Mohamed Helmy

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

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 Uğur Doğrusöz

Joseph Stahl - Vanderbuilt University, Nasville, TN, USA

Tutorials for Cytoscape.js
Mentored by Max Franz

Ashish Tiwari - Arizona State University, Tempe, AZ, USA

Cytoscape command line scripting enhancements
Mentored by Scooter Morris

Zhaoyuan Zoe Xi - University of California Los Angeles, Los Angeles, CA, USA

Extending Cytoscape.js: Addition of Clustering Algorithms
Mentored by Mike Kucera

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

2014 (17/18 passing students, 94%)

Ankit Agarwal - Manipal University, Manipal, India

Virtual Cell iPhone App Enhancements
Mentored by Jim Schaff

Arman Aksoy - Memorial Sloan-Kettering Cancer Center, New York, NY, USA

Pathway Database Converters for the Expansion of Pathway Commons
Mentored by Augustin Luna

Srikanth Bezawada - Birla Institute of Technology and Sciences, Pilani, India

Implementing TieDIE algorithm as a Cytoscape App
Mentored by Evan Paull

Alex Crits-Christoph - Johns Hopkins University, Baltimore, MD, USA

Developing An Interface For The Cancer Network Altering Variant Database
Mentored by Mohamed Helmy

Kirtan Dave - Sardar Patel University, Vallabh Vidyanagar, India

New Features for Interference App
Mentored by Cristian Munteanu

Shaik Faizaan - Birla Institute of Technology and Sciences, Pilani, India

Porting Interference App to Cytoscape 3
Mentored by Giovanni Scardoni

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

Jimmy Morzaria - Birla Institute of Technology and Sciences, Pilani, India

Network Analysis Enhancements
Mentored by Jason Montojo

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

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

Rohan Saxena - Birla Institute of Technology and Sciences, Pilani, India

PathVisio Plugin to Load Additional Information about Data Nodes
Mentored by Martina Kutmon

Adam Shaw - University of Chicago, Chicago, IL, USA

Hierarchical Models in Segway
Mentored by Michael Hoffman

Georg Summer - Maastricht University and TNO, Maastricht, The Netherlands

Connecting Neo4j and Cytoscape
Mentored by Barry Demchak

Abhiraj Tomar - University of Southern California, Los Angeles, CA, USA

Implementation of new clustering techniques into Cytoscape
Mentored by Scooter Morris

Truhin Alexandr - Technical University of Moldova, Chisinau, Moldova

Pathvisiojs Diff Viewer
Mentored by Anders Riutta

2013 (14/15 passing students, 94%)

Ankit Agarwal - Manipal University, Manipal, India

iPhone application for viewing of public/private results in the Virtual Cell
Mentored by Jim Schaff

Truhin Alexandr - Technical University of Moldova, Chisinau, Moldova

Bird's eye view pan control for Cytoscape.js
Mentored by Christian Lopes

Istemi Bahceci - Bilkent University, Ankara, Turkey

Specialized Layout Algorithm for SBGN Process Description Diagrams
Mentored by Uğur Doğrusöz

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

Sri Harsha - Keshav Memorial Institute of Technology, Hyderabad, India

SBML Importer Plugin for PathVisio
Mentored by Anwesha Dutta

Gerardo Huck - National University of Rosario, Rosario, Argentina

Compound Graph Layout Algorithm for Cytoscape.js
Mentored by Max Franz

Ritisha Laungani - Birla Institute of Technology and Sciences, Pilani, India

Modeling and Visualizing Cell Signaling Networks with SigViz
Mentored by Graham Johnson

Christ Leemans - University of Maastricht, Maastricht, The Netherlands

Automated pathway-creation plugin for PathVisio
Mentored by Andra Waagmeester

Alvin Leung - McGill University, Montreal, Canada

Implementing a Cytoscape 3.0 app for the HyperModules algorithm
Mentored by Gary Bader

Diego Magagna - Verona University, Veneto, Italy

Multiplication of nodes and directed graphs in Cytoscape 3
Mentored by Giovanni Scardoni

Jimmy Morzaria - Birla Institute of Technology and Sciences, Pilani, India

Visualization of Dynamic Graphs in Cytoscape
Mentored by Jason Montojo

Sravanthi Sinha - Keshav Memorial Institute of Technology, Hyderabad, India

WikiPathways client plugin for PathVisio
Mentored by Martina Kutmon

Abhiraj Tomar - Birla Institute of Technology and Sciences, Pilani, India

Implementation of Fuzzy Clusters in Cytoscape
Mentored by Scooter Morris

Li Zhang - Jilin University, Changchun, China

Identifier Mapping App for Cytoscape 3.0
Mentored by Chao Zhang

2012 (16/16 passing students, 100%)

Istemi Bahceci - Bilkent University, Ankara, Turkey

SBGN-Complaint Views for Cancer Genomics Networks
Mentored by Uğur Doğrusöz

Khushi Chachcha - University of British Columbia, Vancouver, Canada

GeneMANIA plugin for MedSavant
Mentored by Marc Fiume

Neil Dhruva - Birla Institute of Technology and Science, Pilani, India

Data summary of tables in Cytoscape
Mentored by Samad Lotia

Yue Dong - University of Toronto, Toronto, Canada

Cytoscape App Manager, Cytoscape Web WebGL Renderer and Layouts, Presentation API Testing
Mentored by Jason Montojo

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

Rianne Fijten - University of Maastricht, Maastricht, The Netherlands

Plugin for metabolite information in Pathvisio
Mentored by Egon Willighagen

Jake Fried - University of Maryland, College Park, MD, USA

Understanding Complex Pathways using User Data and Web Services in PathVisio
Mentored by Augustin Luna

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

Michael Kirby - University of California, San Diego, CA, USA

A Direct Interface Between R and Cytoscape
Mentored by Mike Smoot

Praveen Kumar - Jawaharlal Nehru Technological University, Hyderabad, India

Pathway Comparison in PathVisio
Mentored by Martina Kutmon

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

David Shih - University of Toronto, Toronto, Canada

Porting HOPACH cluster algorithm into clusterMaker
Mentored by Scooter Morris

Sinan Sonlu - Bilkent University, Ankara, Turkey

Layout Algorithms for New Cytoscape Web
Mentored by Uğur Doğrusöz

Chao Zhang - University of Missouri, Columbia, Missouri

Ontology-based Network Visualization and Analysis
Mentored by Alexander Pico

Yigang Zhou - Wuhan University, Wuhan, China

Visualizing Semantic Data Landscapes with Cytoscape 3.0
Mentored by Andra Waagmeester

2011 (8/10 passing students, 80%)

Andrew Brook - University of Toronto, Toronto, Canada

Integrate Pathway Visualization and Analysis into Savant
Mentored by Marc Fiume

Kumar Chandan - Keshav Memorial Institute of Technology (KMIT), Hyderabad, India

Real-time Validation Framework for Pathvisio
Mentored by Augustin Luna

Yue Dong - University of Toronto, Toronto, Canada

Cytoscape Web - HTML5 Prototype
Mentored by Jason Montojo

Gerardo Huck - National University of Rosario, Rosario, Argentina

Connecting Cytoscape with igraph
Mentored by Gang Su

Martina Kutmon - University of Maastricht, Maastricht, The Netherlands

New PathVisio Plug-in Manager
Mentored by Martijn van Iersel

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

Marek Zaluski - Concordia University, Montreal, Canada

HTML5 prototype for Cytoscape Web
Mentored by Christian Lopes

Chao Zhang - University of Missouri, Columbia, MO, USA

GOLayout: Network partitioning and layout driven by GO ontology
Mentored by Alexander Pico

2010 (10/10 passing students, 100%)

Chetan Bansal - Birla Institute of Technology and Science Pilani, Goa, Hyderabad, India

Exploring relations between pathways on WikiPathways
Mentored by Thomas Kelder

Gerardo Huck - National University of Rosario, Rosario, Argentina

Improving Cytoscape's Labels Experience
Mentored by Mike Smoot

Dazhi Jiao - Indiana University, Bloomington, IN, USA

Expression Data Reader plugin for Cytoscape
Mentored by Alexander Pico

Bing Liu - National University of Singapore, Singapore, Singapore

Improve the PathVisio User Interface
Mentored by Kristina Hanspers

Kozo Nishida - Nara Institute of Science and Technology, Nara, Japan

KEGG global map browser and its integration to Processing visualizer
Mentored by Keiichiro Ono

Layla Oesper - University of Wisconsin, Madison, WI, USA

Using NLP Techniques to Create a Semantic Network Summary for Cytoscape
Mentored by Ruth Isserlin

Leontius Pradhana - National University of Singapore, Singapore, Singapore

Reactome-Wikipathways Round-trip Format Converter
Mentored by Guanming Wu

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

Avinash Thummala - IIIT-H, Hyderabad, India

Creating a CyAnnotator and improving CyAnimator
Mentored by Scooter Morris

Tomithy Too - National University of Singapore, Singapore, Singapore

Proposal for the Implementation of Edge-Weighted Force Directed layout for Cytoscapeweb
Mentored by Christian Lopes

2009 (9/10 passing students, 90%)

Chetan Bansal - Birla Institute of Technology and Science Pilani, Goa, Hyderabad, India

Ontologies for Wiki Pathways
Mentored by Alexander Pico

Chinmoy Bhatiya - Denison University, Granville, OH, USA

Phylogenetic tree plugin for Cytoscape
Mentored by Pen-Liang Wang

Adem Bilican - University of Maastricht, Maastricht, The Netherlands

Biopax plugin(import, layout, export) for PathVisio
Mentored by Martijn van Iersel

Stephen Federowicz - UCSC, Santa Cruz, CA, USA

CyAnimator: A general purpose animation tool for Cytoscape
Mentored by Scooter Morris

Jianjiong Gao - University of Missouri, Columbia, MO, USA

ID mapper API and plugin for Cytoscape
Mentored by David States

Gerardo Huck - National University of Rosario, Rosario, Argentina

Cytoscape GPU Assisted Graph Layout Plugin
Mentored by Daniel Abel

Helen Xuemin Liu - Iowa State University, Ames, Kansas City, MO, USA

Superpathways in Cytoscape
Mentored by Thomas Kelder

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%)

Daniel Abel - Eotvos University, ELTE, Budapest, Hungary

Implement long-standing cytoscape wishlist features in cytoscape core
Mentored by Mike Smoot

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

Jianjiong Gao - University of Missouri, Columbia, MO, USA

Advanced network merge for Cytoscape
Mentored by Keiichiro Ono

Dazhi Jiao - Indiana University, Bloomington, IN, USA

Integration of Cheminformatics Tools in Cytoscape
Mentored by Scooter Morris

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

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

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