Projects per cycle
National Resource for Network Biology (NRNB), 2016 to 2026
View as table
| Projects | |
|---|---|
| 2016 | 15 |
| 2017 | 20 |
| 2018 | 10 |
| 2019 | 11 |
| 2020 | 15 |
| 2021 | 13 |
| 2022 | 8 |
| 2023 | 8 |
| 2024 | 11 |
| 2025 | 8 |
| 2026 | 7 |
PROJECTS
National Resource for Network Biology (NRNB) GSoC projects
126 accepted projects across 11 cycles, 2016 to 2026. Each one links to its contributor, mentors and code.
Projects listed
126
Across 11 cycles
In GSoC 2026
7
8 in 2025
Busiest cycle
2017
20 projects
Mentors named
129
Across all listed projects
First cycle
2016
Latest 2026
Implement a Data-Driven Visual Attribute Mapping System in GraphSpace
Akriti agrawal
This project aims to implement a Visual Attribute Mapping System that enables users to automatically map node and edge attributes to visual...
openPIP 2 Modernizing the Open Source Protein Interaction Platform
hamid-ananda
openPIP is an open-source platform for hosting and visualizing protein-protein interaction (PPI) data. The current version is built on a PHP 5.6 /...
Enhancing VCell AI Platform
Kartik Deshpande
VCell-AI is an AI-powered platform for discovering, analyzing, and exploring biological models from the VCell database. While the platform already...
Proposal for the Unified App Registry for Cytoscape App Store
Kevin Zhu
Currently, the Cytoscape App Store only supports plugins for the Cytoscape Desktop App. Since a web version of Cytoscape is available, web plugins...
Evaluating and Improving Symbolic Regression Methods for Biological Network Dynamics
Norma Citlalcue Perez Rosas
This project aims to improve and evaluate symbolic regression methods for discovering interpretable mathematical models of biological network...
ML Models that use SBOL for DNA annotation by Shreeya
Shreeya456
Developing a scalable and reproducible research pipeline within SeqTrainer for bacterial DNA sequence modelling and annotation using SBOL-based...
Direct Integration of PathVisio with WikiPathways GitHub
Snehashree Prusty
This project aims to develop a Direct GitHub Integration Plugin for PathVisio to transform the pathway curation workflow from outdated systems to the...
SBOL2 SBOL3 Convertor Utility
__Harsh_Sharma__Mentored by jakebeal, Gonza10V
The Synthetic Biology Open Language (SBOL) serves as a vital community standard for representing biological designs, with version 3.1 offering mature...
SeqTrainer - creating datasets from SynBioHub to aid researchers in creating machine learning models
cywongMentored by Chris Myers, Gonza10V
In the realm of synthetic biology, there is a significant source of data in the form of models, genetic sequences, regulatory networks, and...
Developing a Highly Efficient Numerical ODE Solver in the Systems Biology Simulation Core Library
Ayush BaranwalMentored by Akira Funahashi, Arthur Neumann, Taichi +1
The field of computational biology depends significantly on mathematical modeling to simulate complex biological simulations, often involving...
CySBML Reloaded: Smarter, Simpler, Automated
Hikmet Emre KayaMentored by Matthias König, Prof. Dr. Andreas Dräger
CySBML Reloaded: Smarter, Simpler, Automated focuses on upgrading CySBML — a Cytoscape app for visualizing computational models encoded in SBML. The...
Enhancing SBOannotator with LLM Integration & Dynamic Term Retrieval
Jiahui HuMentored by Nantia Leonidou, Prof. Dr. Andreas Dräger
This proposal aims to transform SBOannotator from a static, hard-coded tool into a dynamic, intelligent system for annotating SBML models with...
VCell-AI: AI Analysis & Querying Platform
Kacem MathlouthiMentored by MichaelBlinov, Jim Schaff, Mindy Zhang
This project aims to build an intelligent chatbot and web interface that allows researchers to query and explore models from the VCell BioModel...
Enhancing the Systems Biology Simulation Core Library (SBSCL) with a Solver-Agnostic Framework...
Michael-GaasMentored by Matthias König, Prof. Dr. Andreas Dräger
This project addresses the current incompatibility of the Systems Biology Simulation Core Library (SBSCL) with modern computing architectures,...
LLM-Powered Interactive Chat Interface for CellMinerCDB with GraphRAG Integration
Milit S PatelMentored by AugustinL, Yoshitaka Inoue
This project will develop an intelligent chat interface for CellMinerCDB, a cancer genomics database, using GraphRAG (Graph Retrieval-Augmented...
GPML support in Newt
Aditya SainiMentored by Yihang Xin, Hasan Balcı, Martina Summer-Kutmon
The goal of this project is to add new functionalities to Newt to be able to create biological maps in GPML format from scratch or edit existing...
Machine Learning Support for Constructing Newt SBGN Maps
Umut Utku ERŞAHİNCEMentored by AugustinL, Ugur Dogrusoz, Adrien Rougny
In this proposal, I explain the machine learning support I aim to implement to generate SBGN maps. I am planning to make an API connection to a...
Integration of complexity score functions into the iGEM DNA kit distribution workflow
Johan GuillenMentored by jakebeal, Gonza10V
The goal is developing an updated workflow that uses the existing iGEM distribution structure to integrate a synthesizability assessment of genetic...
ASCETIC Vision
Nada MohamedMentored by Marco Antoniotti, Daniele, Alex Graudenzi
This project aims to enhance the accessibility and usability of the ASCETIC framework, which interprets tumor evolutionary signatures crucial for...
Integration of GRN inference algorithms using single cell multi-omics data to BEELINE
BB Vishnu MadhavMentored by Marco Antoniotti, Yiqi Su, Maryam-H
BEELINE is a bench marking tool that evaluates different methods and models that infer Gene Regulatory Networks (GRN) from Single cell gene...
COBRAxy: COBRA and MaREA4Galaxy
Luca MilazzoMentored by Marco Antoniotti, Chiara Damiani, Alex Graudenzi
MaREA4Galaxy is a user-friendly tool designed to facilitate the characterization and graphical comparison of sample groups exhibiting distinct...
Implement AWS DevOps Pipeline for Image Deployment for Graphspace
Deep PoharkarMentored by Yash Agarwal_, Mahesh Kasbe
Project mainly focuses on automating image deployment to an EC2 instance via an AWS DevOps pipeline. Key tasks involve setting up an AWS account with...
Large Language Model-based creation of knowledge graph from a publication
Favour JamesMentored by AugustinL, dexterpratt
This project proposes the development of a Python web application that utilizes Large Language Models (LLMs) for extracting, transforming, and...
Using Foundation Model: scGPT for Gene Regulatory Network Inference
Faizal RahmanMentored by Nure Tasnina, Blessy Antony
The project aims to develop a robust pipeline for assessing the performance of foundation models, specifically focusing on scGPT, in generating...
Cytoscape layout plugin to support Cytoscape.js layouts
Tushar ChoudharyMentored by Scooter, Ugur Dogrusoz, Hasan Balcı
Cytoscape Desktop Application serves as a powerful tool for network analysis and visualization. However, its layout options are limited compared to...
Improvement Of openPIP (Data upload & Visualization)
Mohamed SoudyMentored by Mohamed Helmy, Diogo Pellegrina
OpenPIP platform is typically necessary alongside a research paper detailing experimental data, alongside depositing the data into a standard...
Automate Cytoscape.js release process using GitHub Actions
Akash MondalMentored by Gary Bader, Max Franz, Michael Kucera +1
Cytoscape.js is an open-source JavaScript-based graph theory library that can be used for graph analysis and visualisation. It contains many useful...
Generate Example Dataset for PyTorch Geometric Based on Pathway Commons and Prototype
Favour JamesMentored by AugustinL, Yoshitaka Inoue
The main goal of this project is to create a PyTorch Geometric(PyG) dataset by integrating the cBioPortal and Pathway Commons datasets and provide a...
Implement a R Shiny module for Network Analysis in CellMinerCDB
Siddharth ChaudharyMentored by AugustinL
CellMinerCDB provides a web-based resource for integrating multiple forms of pharmacological and genomic analyses, and unifying the richest cancer...
Develop new features for Cytoscape App-cyPlot
Kartik Kumar PawarMentored by Alex Pico, Scooter, Yihang Xin
This project involves updating cyPlot(a Cytoscape app written in JAVA) which provides the ability to plot data through GUI or CyCommands/REST. CyPlot...
Development of a Cytoscape App for microbe-microbe association networks
Ermis DelopoulosMentored by Scooter, Haris Zafeiropoulos, Yihang Xin
Microbial associations play a fundamental part in deciphering underlying mechanisms of microbial communities. A series of algorithms have been...
Convert CellBox Tensorflow code to Pytorch
Phuc NguyenMentored by AugustinL, Bo Yuan
CellBox is a model for predicting cell states under drug perturbations, whose code base was originally written in Tensorflow 1. Since Tensorflow 1...
Setting up the CI/CD Pipeline using Github Actions on GraphSpace
Mahesh KasbeMentored by Yash Agarwal_, Daniyal Jahan
Currently the Graphspace code repository has a lot of mismatched dependency issues & consist no automating techniques in their repository to release...
Supporting Pathway Commons and ssGSEA in clusterProfiler
JIGYASA GUPTAMentored by AugustinL, Guangchuang Yu
clusterProfiler is an efficient package that provides a universal interface for gene functional annotation from a variety of resources and is...
SBML-MINERVA support in Newt
Selbi EreshovaMentored by Ugur Dogrusoz, Marco Antoniotti, A. Mazein
Currently, the Newt editor supports Systems Biological Graphical Notation (SBGN) and Simple Interactive Format (SIF) formats while also allowing...
Create a Pipeline from data extraction to execution of GNN based Drug Response Prediction
Yoshitaka InoueMentored by AugustinL, Vishwesh Kulkarni, Judy Shen
The use of machine learning models in medicine is expanding, but there are still undergoing due to the interpretability. One useful example which has...
High-throughput simulation for computational cell biology with Cloud-COPASI
Fizza RubabMentored by Hasan Baig, Pedro Mendes
Customized SSH Authentication Free Implementation of the Cloud-COPASI for UConn users: The project proposal aims to create a customized version of...
Updates to the Enrichment Table App
Akash MondalMentored by Alex Pico, Indraneel, Yihang Xin
This proposal aims to implement new features to the Enrichment Table App. The major changes were adding Ring Charts, prediction of gene id column and...
Adding visualization of protein-complex interaction to OpenPIP
Aniket RanjanMentored by Gary Bader, Mohamed Helmy, Vishwesh Kulkarni
OpenPIP (Open Source Protein Interaction Platform) is an open-source software package for hosting protein-protein interaction (PPI) data based on the...
Conversion between GenBank and SBOL3
Mohit MakwanaMentored by Tom Mitchell, jakebeal, Vishwesh Kulkarni
The SBOL-Utilities repository is a python library that provides many useful methods and utilities on top of the main PySBOL3 implementation of SBOL3....
NetBoxR Updates
Sara JMentored by AugustinL, Eric Liu
netboxr is an R package for the automated discovery of biological process modules by network analysis. The project involves updating netboxr...
Create Jupyter Notebooks showcasing COMBINE Standards
Aditya SinghalMentored by AugustinL, Matthias König, Vishwesh Kulkarni
The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of various community standards and formats in...
Enhancing ABioTrans Plus using Gene Expression Omnibus database and adding analysis report
Javed AliMentored by Mohamed Helmy, buithuytien1313
This project aims to add new features to ABioTrans Plus(GeneCloudOmics) that includes the direct import of gene expression data from Gene Expression...
Simple Enrichment Tool for Analysis
Indraneel GhoshMentored by Yihang Xin, Scooter Morris, Alex +2
Cytoscape is a highly popular open source bioinformatics software platform for visualizing, analyzing, and publishing graphs or networks representing...
Develop a Cytoscape App for the Casual Path Algorithm
Pritam SahaMentored by Augustin Luna, Ozgun Babur, Yihang Xin
The project is marked as Issue #169 in GitHub. The main goal of this project is to visualize the network which is generated from the Casual Path...
Enhancing the admin panel of openPIP
Aniket RanjanMentored by Gary Bader, Mohamed Helmy
This project aims to add improvements in the admin panel of openPIP that is used to upload data and files, post announcements and change global...
Local DB support for SBGN maps in Newt
Pankaj YadavMentored by Augustin Luna, Alexander Mazein, Ugur Dogrusoz
Newt is a web-based tool to analyze biological maps in standard formats such as PD and AF languages of SBGN, SBML, and SIF. This project aims to...
Expand ModelBricks.org and VCell API
Noah Liguori-BillsMentored by Ann Cowan, Frank Morgan, Michael Blinov
ModelBricks is a tool for bioinformatics researchers that allows users to browse, view, and download detailed models of biological processes. I...
SBML Simulator in Rust
Pranav BallaneyMentored by Akira Funahashi, KAITO II, Akito Tabira +2
Over the last few years, the programming language Rust has seen a surge in popularity. This has primarily been the case due to its more robust memory...
Implementing multiple clustering algorithms and dimensionality reduction techniques on clusterMaker2
Maija UtriainenMentored by Scooter Morris, Alex, Yihang Xin
Implementing following dimensionality reduction techniques and clustering algorithms to clusterMaker2: UMAP, t-SNE, PCA, PCoA, Louvain, Walktrap,...
Adding Multi-omics data support to ABioTrans Plus
Mohamed Soudy-1Mentored by Mohamed Helmy, buithuytien1313
ABioTrans Plus is a web server for transcriptome data analysis and visualization. It supports the analysis of microarray and RNASeq data and performs...
SBML4Humans - Interactive SBML Report for Humans
Sankha DasMentored by Matthias König, Ralf Steuer
Systems Biology Markup Language (SBML) is a standard format for the representation and exchange of biological models between computers. The...
Develop GUI for ImageJ groovy script calling VCell API
NIKITA MAHOVIYAMentored by Ann Cowan, Frank Morgan, Michael Blinov
We have to create a service for VCell users that allows Fiji/ImageJ scripting to directly access the VCell client. We have to expand this service...
TumorComparer, updated version
Siras HakobyanMentored by Rileen Sinha, Augustin Luna
TumorComparer, updated version The TumorComparer is a computational method for the comparison of different cancer types with cancer cell lines by...
PD to AF conversion facility in Newt
Can AlpayMentored by Augustin Luna, Alexander Mazein, Ugur Dogrusoz
Newt supports the Process Description (PD) and the Activity Flow (AF) graphs of SBGN. However, there is no conversion between these two graphs in...
Generating detailed SBOL representation of genetic logic circuits along with improved designing capability, and Java-Python conversion.
Mudasir ShaikhMentored by Hasan Baig, Ritwik
GeneTech allow users to develop genetic logic circuits only by specifying a Boolean function. The tool first performs Boolean optimisation, followed...
Implementation of SBML-JSON converter and SBML-JSON scheme
HemantMentored by Matthias König, Lucian Smith, Andreas Dräger +1
The Systems Biology Markup Language (SBML) is the main language for representation and exchange of computational models in biology. JSON is the main...
Adding Bio-Statistical Machine Learning Models and Graphical visualization to ABioTrans V2
Rahul AgrawalMentored by Kumar Selvarajoo, Mohamed Helmy
ABioTrans is a bio-statistical/informatics tool, developed in R for gene expression analysis. The tool allows the user to directly read RNA-Seq data...
Enhance Web Interface for Natural-Language Processing Extracted Interaction Network
Priti ShawMentored by RohitC, Benjamin Gyori, Augustin
Goal: The goal is to expand on the web interface and the data generation pipeline developed in 2019. Overview: Continuing to the already done work,...
Development of a system that generates spatial SBML models using deep learning
Medha BhattacharyaMentored by Kaito Ii, Akira Funahashi, tokkuman
This project aims at creating and implementing a system that automatically generates various spatial SBML models by comprehensively segmenting...
Developing a tool for implementing clustering algorithms to Cytoscape app ClusterMaker2
Maija UtriainenMentored by Dexter Pratt, John "Scooter" Morris, ALEXANDER PICO
In this project, I will develop a tool in Cytoscape app ClusterMaker2 that helps implementing new clustering algorithms in the app from inside...
LACE-View : A Visualizer for Longitudinal Clonal Trees
Bhavesh NarraMentored by Marco Antoniotti, Daniele, Alex Graudenzi
LACEview is a visualization tool for LACE (Longitudnal Analysis of Cancer Evolution) developed by a team at BIMIB. The tool is for R visualization...
Improving compmodelmatch.org
Sahil JhaMentored by Danny Fryer, Michael Blinov
This project intends to make several improvements to compmodelmatch platform which will improve its performance and also add features such as ORCID...
Implement a comment/discussion system in GraphSpace
Yash Agarwal_Mentored by Daniyal Jahan, Aditya Bharadwaj, T. M. Murali
The aim of this project is to implement a real-time comment/discussion and reaction system that will allow users to comment on graphs and discuss...
Enhancing PathwayMapper in cBioPortal and PathwayMapper editor
Merve KılıçarslanMentored by Ugur Dogrusoz, ALEXANDER PICO, Onur Sumer +1
Pathways are created by selecting certain genes and studies then displayed in the PathwayMapper tab in the cBioPortal. However, not every page in...
Redevelop Model Bricks code base architecture
Saksham RaghuvanshiMentored by Ann Cowan, Frank Morgan, Michael Blinov +1
Model Bricks project is an effort focused on describing recurring patterns in biological networks. These patterns are described as small VCell models...
Simulation of systems biology models in Java: support for new features
Hemil PanchiwalaMentored by Shalin Shah, Matthias König, Mykola Zakharchuk +1
Systems biology studies the mechanisms underlying complex biological processes as integrated systems of many interacting components. Modeling...
Integrating RRPlugins with libRoadRunner
Debashish RoyMentored by Kiri Choi, Herbert Sauro
LibRoadrunner is a high-performance SBML based simulator that uses LLVM to generate very efficient runtime code. This enables LibRoadrunner to...
Integration of sequence visualization into SynBioHub
Linhao MengMentored by Geoff Baldwin, Christopher Myers
As a design repository for Synthetic Biology, SynBioHub facilitates the sharing and searching for information, combining data from a variety of...
Spreadsheet Plug-in for SynBioHub
Isabel MarleenMentored by Christopher Myers, JVM, jakebeal
Synthetic Biology is a discipline that connects many disciplines and heterogeneous researchers. To be useful as a tool, a platform such as SynBioHub...
Implement a machine-readable graph legend interface
Ayush Ranjan LohaniMentored by Aditya Bharadwaj
The overall goal of this project is to implement a machine-readable graph legend interface and extend the API to add, modify and remove legend data...
Integrating RRPlugins with libRoadRunner and devloping Differential Evolution optimizer plugin
Debashish RoyMentored by Herbert Sauro
LibRoadrunner is a high performance SBML based simulator that uses LLVM to generate very efficient runtime code. This enables LibRoadrunner to...
Extending ModelPolisher to a universal model annotation tool
Kaustubh TrivediMentored by Matthias König, Thomas Zajac
ModelPolisher is a model annotation tool for the BiGG Models Knowledgebase. Annotations enhance the reusability and interoperability of biological...
CiSE layout as a Cytoscape.js extension and an automated layout web service for popular Cytoscape.js layout extensions
Perman AtayevMentored by Ugur Dogrusoz
Automated layout web service with an integrated converter, to change the format of the data, would be of great use for people who want to quickly and...
New Build System for InSilico
Nikhil GhodkeMentored by Roman, Andreas Dräger
InSilico is an extensible editor which can be used for manipulating and analyzing many different file types, SBML files in particular. The current...
Simulator for Systems Biology
Robin SimonotMentored by Akira Funahashi
Develop a simulator which will support all the features of SBML core specification Implement a code so that the simulator can pass testcases which...
Web Interface for NLP Extracted Interaction Network
Rohit R. ChattopadhyayMentored by Augustin Luna
An application for users to access biological data extracted from biomedical literature. Project Mentor Augustin Luna Objectives Easy search...
Validation of spatial systems biology models in Java
Bhavye JainMentored by Thomas Hamm, Nicolas Rodriguez
The spatial extension for SBML provides support for describing processes that involve a spatial component. This project seeks to implement validation...
App Store for Cytoscape Apps
Sarthak SrivastavaMentored by AlexanderPico
I am interested in the project “Appstore for the Cytoscape App” with Alex Pico, Barry Demchak and Scooter Morris as its mentor. My goals for the...
BridgeDb Major Release
Manas AwasthiMentored by Egon Willighagen
BridgeDb is a platform used for identifier mapping in WikiPathways and PathVisio with support for various languages like as a Cytoscape plugin, as an...
GraphSpace: Diffs for graphs
Daniyal JahanMentored by T. M. Murali
The goal of this project ‘Diff for Graphs’ is to implement a graph comparison functionality which will allow users to compare two or more graphs that...
Develop cyTRON/JS: a backend and a cytoscape.js visualizer for cancer progression models
Lucrezia PatrunoMentored by Daniele Ramazzotti, Marco Antoniotti
This project aims at developing a tool which should provide an interactive visualization of the cancer progression models produced by the R library...
Implement SBML Array Support in libRoadRunner
Vineeth ChelurMentored by Chris Myers, Herbert Sauro, Leandro Watanabe
LibRoadrunner is a high-performance SBML based simulator for Systems and Synthetic Biology that uses LLVM to generate very efficient runtime code....
Integrating CAD and CAM tools for automating a synthetic biology workflow
Prem Prakash SinghMentored by Chris Myers, Michael Zhang, Ernst Oberortner
Integrated Build Software Optimisation Tools (BOOST) with SBOLDesigner. SBOLDesigner is a CAD tool for creating and manipulating the sequences of...
Improvements for Newt, a Cytoscape.js based SBGN editor
Ahmet ÇandıroğluMentored by Ugur Dogrusoz, Alexander Mazein
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...
PathwayMapper Improvements and Integration into cBioPortal
Kaan SancakMentored by Ugur Dogrusoz, Onur, JJ Gao
While the network visualization module in cBioPortal is a powerful exploration tool, most biologists are more comfortable with the kind of...
App Store for Cytoscape Apps
Sarthak SrivastavaMentored by Scooter Morris, Alexander Pico
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...
GraphSpace: Git for graphs
DaniyalMentored by Aditya Bharadwaj, Jing Cui
GraphSpace is a web-based platform where collaborating research groups can use a user-friendly interface to create, interact and share networks....
Upgrading Ontology Tagging at WikiPathways
Dara AkdagMentored by Martina Summer-Kutmon, Alexander Pico
Ontologies are an integral part of our scientific progress. The ability to share common definitions is crucial to answering questions, thus, an...
Simulating systems biology models in Java
ShalinMentored by Hannes Planatscher, Nicolas Rodriguez, Matthias König +1
Computational models of biological systems play an important role in advancing science as they give insights about the biology without the need for...
Rendering Complex Genetic Design with DNAplotlib for a Beautiful Visualization of Genetic Circuit
Sunwoo KangMentored by Bryan Bartley, Thomas Gorochowski
Visualizing genetic circuits is essential in the field of synthetic biology. These genetic designs often involve complex representation of modular...
Interconversion of the SBML and SBGN Modelling Languages using Semantics of Logic
Haoran YuMentored by Nicolas Rodriguez, Sarah Keating
Systems biology researchers study the network of molecular interactions within a biological system and publish the deduced models in a diagram...
Cytoscape.js Extension for Querying Large Networks
Hasan BalcıMentored by Ugur Dogrusoz, Ozgun Babur
Traversal-based graph algorithms are good at extracting “subgraphs of interest” when applied to large networks. However, applying known algorithms...
Extending the IBW Biocompilation Interface with SBOL and SBML Import/Export Capabilities
bodunMentored by Chris Myers, Harold Fellermann, Vishwesh Kulkarni
The Infobiotics Workbench (IBW) is a synthetic biology design tool with three major functionalities: stochastic simulations, which mimic the...
PiType: A Protein Interaction Prediction Cytoscape App
MWranaMentored by Srikanth, Florian Goebels
PiType is an already existing protein-protein interaction classifying tool created by my mentor. It currently exists as both a web app and a...
Improvements in Tool for Curating Biological Maps in SBGN
Ilkin SafarliMentored by Ugur Dogrusoz, Alexander Mazein
SBGNViz is a Cytoscape.js based library for viewing biological maps in Systems Biology Graphical Notation (SBGN) notation. ChiSE is a library based...
OpenGL-accelerated Renderer for Cytoscape 3
MENGHE ZHANGMentored by Scooter Morris, Vishwesh Kulkarni, bdemchak
Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways. It integrates these networks...
WikiPathways Pathway Presenter
jcbwndsrMentored by Egon Willighagen, Anders Riutta, Vishwesh Kulkarni +1
WikiPathways is an open and collaborative platform for sharing biological pathway information. It features an interactive diagram that aids the user...
Implement Network Quantity Information measure in CentiScaPe #64
Ivan BestvinaMentored by Giovanni Scardoni
CentiScaPe is a Cytoscape application used to calculate a number of different node centralities of an optionally weighted network, both directed and...
libGPML library to read and write GPML files
Saurabh KumarMentored by Martina Summer-Kutmon, Alexander Pico
libGPML Currently it is required to include the whole PathVisio core module which is much bigger and already contains PathVisio specific...
Develop a web service which provides simulation / steady state analysis / parameter estimation with SBML models
Takahiro YamadaMentored by Kaito Ii, Andreas Dräger
In systems biology, it is very important to formalize the model for biological phenomenon and analyze based on this model basically constructed by...
Notification system for GraphSpace
Melvin MathewMentored by Mitch Wagner, Aditya Bharadwaj, T. M. Murali
GraphSpace is an user-friendly web-based platform that collaborating research groups can utilize for storage, interaction, and network sharing. A...
Developing a web interface for DoMo-Pred
Long ZhangMentored by Mohamed Helmy, Vishwesh Kulkarni, Gary Bader +1
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...
Developing a Cluster Computing Framework for Dynamical Modeling
Shaik AsifullahMentored by Kyle Medley, Matthias König
Integrating the existing Tellurium project with Apache Spark and by which the computations or simulations can be run in parallel. Developing an API...
Implement GeneMANIA in Julia for High-performance Computing
Guodong XuMentored by Gary Bader, Shraddha Pai
The aim of the project is to Implement GeneMANIA in Julia to optimize netDx for high-performance computing. The current Java-based implementation of...
Roadmap to create a WebApp for the Enrichment Map Using Cytoscape and RESTful services
Bhavesh NarraMentored by Jeffrey Wong-1, Max Franz, cannin
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...
Implementation of a Python Library for GraphSpace RESTful APIs
Sandeep MahapatraMentored by Aditya Bharadwaj, T. M. Murali
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...
Develop a Synthetic Biology Publication Workflow that Leverages the Synthetic Biology Open Language
Zach ZundelMentored by Chris Myers, jm, Anil Wipat
A large goal of both the SBOL and synthetic biology communities is to develop a useful and comprehensive workflow from experiment to publication....
Cytoscape app for GraphSpace (CyGraphSpace)
Rishabh SethiMentored by Scooter Morris, Aditya Bharadwaj, T. M. Murali
The overall goal of the project is to create a Cytoscape app (CyGraphSpace) for syncing networks from Cytoscape to GraphSpace and vice-versa....
Adding support for PSIMI-TAB format to the Disease Variant Impact (DV-IMPACT) Database
Raghav JajodiaMentored by Gary Bader, Mohamed Helmy
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...
cyTRON: a Cytoscape app for the visualization of evolutionary trajectories in cancer progression
Edoardo GalimbertiMentored by Daniele Ramazzotti, Marco Antoniotti, Vishwesh Kulkarni
TRONCO is an R package that implements state-of-the-art algorithms for the inference of cancer progressions with the ultimate goal of understanding...
Principal Coordinate Analysis and t-Distributed Stochastic Neighbor Embedding in clusterMaker2
Supun ArunodaMentored by Scooter Morris
Implement two algorithms which have the ability to do dimensional reduction in cluster Network. Principal Coordinate Analysis and t-Distributed...
Enhance vignettes and plugin use for R package RCy3 for network manipulation using Cytoscape
joooliaMentored by Augustin
Many scientists use networks to visualize complex relationships among species, people, cities, genes, proteins or other subjects. Cytoscape is...
Visualizing genomic alterations in TCGA cancer pathways in cBioPortal
Istemi BahceciMentored by Ugur Dogrusoz
The main goal of this project is to provide a new network view which is capable of visualizing curated TCGA pathways that are more attractive and...
Improving Web Based SBGN Editor SBGNViz.js
Metin Can SiperMentored by Ugur Dogrusoz
SBGNViz.js is an open source web application based on Cytoscape.js to visualize the pathway models represented by SBGN Process Description Notation ....
Java support for Deviser, a code generation system for SBML libraries
Hovakim GrabskiMentored by Frank T. Bergmann
Since SBML Level 3 is being developed as a modular format with optional SBML Level 3 packages are available to extend the focus of the core SBML...
Import graphs in multiple formats and Cytoscape files into GraphSpace
MridulSMentored by Murali
GraphSpace is a tool for storing, sharing, and visualising graphs in order to help collaborative research. Users can upload graphs and share it with...
GSoC: JSBML Validation System
Roman SchulteMentored by Andreas Dräger
The JSBML library is a powerful Java library that gives the use a easy possibility to read, write and manipulate SBML files with Java. Because there...
SBGN-ML and SBML to Escher Converter
Devesh KhandelwalMentored by zakandrewking
Escher is quickly growing in popularity. As Escher currently uses JSON as its data and layout representation format, and most of the community...
Interconvertible Layout program for CellDesigner
KaitoMentored by Akira Funahashi
CellDesigner is a modeling/simulating software capable of visualizing, modeling, and simulating generegulatory and biochemical networks. The key...
Interconversion between the systems biology modeling formats SBML and BioPAX
tramyMentored by Mike Hucka
In the systems biology field, there exists many different standards, with each standard serving for a different purpose. BioPax is a standard used...
Multithread Centiscape (#55)
ibestvinaMentored by giovanniscardoni@gmail.com
CentiScaPe is a Cytoscape application used to calculate a number of different node centralities in a network. All of the centrality calculating...
Cytoscape command line scripting enhancements
Ashish TiwariMentored by Scooter Morris
Cytoscape is a general purpose, open source software platform for complex network data integration, analysis and visualization. Cytoscape’s core...
The Online Resource for Interface Based Interaction Networks (TOR-IBIN) Web Interface
MilesGSOCMentored by Mohamed Helmy
TOR-IBIN will be an online resource for gathering and storing published interface-based protein-protein interactions (PPI). TOR-IBIN aims to make...
Tutorials for Cytoscape.js
joseph.stahlMentored by Max Franz
Tutorials serve as an invaluable way to familiarize oneself with new software. Cytoscape.js currently provides demos but lacks tutorials to tie...
Extending Cytoscape.js: Addition of Clustering Algorithms
Zhaoyuan Zoe XiMentored by Mike Kucera
Cytoscape.js is a graph theory and networks library focused on providing built-in, rich and performant graph models for analysis and data...
Data: Google Summer of Code public archive. Official GSoC archive