National Resource for Network Biology (NRNB)
Developing open source tools for network biology
- 126
- Projects
- 11
- Years accepted
- 7
- In 2026
Projects by year
1262026
7 acceptedShow
Implement a Data-Driven Visual Attribute Mapping System in GraphSpace
Accepted project · by 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
Accepted project · by 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
Accepted project · by 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
Accepted project · by 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
Accepted project · by 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
Accepted project · by 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
Accepted project · by 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aims to develop a Direct GitHub Integration Plugin for PathVisio to transform the pathway curation workflow from outdated systems to the...
2025
8 acceptedShow
The Synthetic Biology Open Language (SBOL) serves as a vital community standard for representing biological designs, with version 3.1 offering mature...
Developing a Highly Efficient Numerical ODE Solver in the Systems Biology Simulation Core Library
Accepted project · by Ayush Baranwal
The field of computational biology depends significantly on mathematical modeling to simulate complex biological simulations, often involving...
SeqTrainer - creating datasets from SynBioHub to aid researchers in creating machine learning models
Accepted project · by cywong
In the realm of synthetic biology, there is a significant source of data in the form of models, genetic sequences, regulatory networks, and...
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
Accepted project · by Jiahui Hu
This proposal aims to transform SBOannotator from a static, hard-coded tool into a dynamic, intelligent system for annotating SBML models with...
The VCell-AI Platform is an AI-powered system for discovering, analyzing, and exploring biomodels, publications, and research papers from the VCell...
Enhancing the Systems Biology Simulation Core Library (SBSCL) with a Solver-Agnostic Framework...
Accepted project · by Michael-Gaas
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
Accepted project · by Milit S Patel
This project will develop an intelligent chat interface for CellMinerCDB, a cancer genomics database, using GraphRAG (Graph Retrieval-Augmented...
2024
11 acceptedShow
- GPML support in NewtAditya Saini
- Machine Learning Support for Constructing Newt SBGN MapsUmut Utku ERŞAHİNCE
- Integration of complexity score functions into the iGEM DNA kit distribution workflowJohan Guillen
- ASCETIC VisionNada Mohamed
- Integration of GRN inference algorithms using single cell multi-omics data to BEELINEBB Vishnu Madhav
- COBRAxy: COBRA and MaREA4GalaxyLuca Milazzo
- Implement AWS DevOps Pipeline for Image Deployment for GraphspaceDeep Poharkar
- Large Language Model-based creation of knowledge graph from a publicationFavour James
- Using Foundation Model: scGPT for Gene Regulatory Network InferenceFaizal Rahman
- Cytoscape layout plugin to support Cytoscape.js layoutsTushar Choudhary
- Improvement Of openPIP (Data upload & Visualization)Mohamed Soudy
2023
8 acceptedShow
- Automate Cytoscape.js release process using GitHub ActionsAkash Mondal
- Development of a Cytoscape App for microbe-microbe association networksErmis Delopoulos
- Generate Example Dataset for PyTorch Geometric Based on Pathway Commons and PrototypeFavour James
- Supporting Pathway Commons and ssGSEA in clusterProfilerJIGYASA GUPTA
- Develop new features for Cytoscape App-cyPlotKartik Kumar Pawar
- Setting up the CI/CD Pipeline using Github Actions on GraphSpaceMahesh Kasbe
- Convert CellBox Tensorflow code to PytorchPhuc Nguyen
- Implement a R Shiny module for Network Analysis in CellMinerCDBSiddharth Chaudhary
2022
8 acceptedShow
- SBML-MINERVA support in NewtSelbi Ereshova
- Create a Pipeline from data extraction to execution of GNN based Drug Response PredictionYoshitaka Inoue
- High-throughput simulation for computational cell biology with Cloud-COPASIFizza Rubab
- Updates to the Enrichment Table AppAkash Mondal
- Adding visualization of protein-complex interaction to OpenPIPAniket Ranjan
- Conversion between GenBank and SBOL3Mohit Makwana
- NetBoxR UpdatesSara J
- Create Jupyter Notebooks showcasing COMBINE StandardsAditya Singhal
2021
13 acceptedShow
- Enhancing ABioTrans Plus using Gene Expression Omnibus database and adding analysis reportJaved Ali
- Simple Enrichment Tool for AnalysisIndraneel Ghosh
- Develop a Cytoscape App for the Casual Path AlgorithmPritam Saha
- Enhancing the admin panel of openPIPAniket Ranjan
- Local DB support for SBGN maps in NewtPankaj Yadav
- Develop GUI for ImageJ groovy script calling VCell APINIKITA MAHOVIYA
- Expand ModelBricks.org and VCell APINoah Liguori-Bills
- SBML Simulator in RustPranav Ballaney
- Adding Multi-omics data support to ABioTrans PlusMohamed Soudy-1
- PD to AF conversion facility in NewtCan Alpay
- SBML4Humans - Interactive SBML Report for HumansSankha Das
- Implementing multiple clustering algorithms and dimensionality reduction techniques on clusterMaker2Maija Utriainen
- TumorComparer, updated versionSiras Hakobyan
2020
15 acceptedShow
- Generating detailed SBOL representation of genetic logic circuits along with improved designing capability, and Java-Python conversion.Mudasir Shaikh
- Implementation of SBML-JSON converter and SBML-JSON schemeHemant
- LACE-View : A Visualizer for Longitudinal Clonal TreesBhavesh Narra
- Enhance Web Interface for Natural-Language Processing Extracted Interaction NetworkPriti Shaw
- Developing a tool for implementing clustering algorithms to Cytoscape app ClusterMaker2Maija Utriainen
- Adding Bio-Statistical Machine Learning Models and Graphical visualization to ABioTrans V2Rahul Agrawal
- Development of a system that generates spatial SBML models using deep learningMedha Bhattacharya
- Simulation of systems biology models in Java: support for new featuresHemil Panchiwala
- Redevelop Model Bricks code base architectureSaksham Raghuvanshi
- Implement a comment/discussion system in GraphSpaceYash Agarwal_
- Enhancing PathwayMapper in cBioPortal and PathwayMapper editorMerve Kılıçarslan
- Improving compmodelmatch.orgSahil Jha
- Integration of sequence visualization into SynBioHubLinhao Meng
- Integrating RRPlugins with libRoadRunnerDebashish Roy
- Spreadsheet Plug-in for SynBioHubIsabel Marleen
2019
11 acceptedShow
- Implement a machine-readable graph legend interfaceAyush Ranjan Lohani
- Integrating RRPlugins with libRoadRunner and devloping Differential Evolution optimizer pluginDebashish Roy
- Extending ModelPolisher to a universal model annotation toolKaustubh Trivedi
- CiSE layout as a Cytoscape.js extension and an automated layout web service for popular Cytoscape.js layout extensionsPerman Atayev
- New Build System for InSilicoNikhil Ghodke
- Simulator for Systems BiologyRobin Simonot
- Web Interface for NLP Extracted Interaction NetworkRohit R. Chattopadhyay
- Validation of spatial systems biology models in JavaBhavye Jain
- App Store for Cytoscape AppsSarthak Srivastava
- BridgeDb Major ReleaseManas Awasthi
- GraphSpace: Diffs for graphsDaniyal Jahan
2018
10 acceptedShow
- Develop cyTRON/JS: a backend and a cytoscape.js visualizer for cancer progression modelsLucrezia Patruno
- Implement SBML Array Support in libRoadRunnerVineeth Chelur
- Integrating CAD and CAM tools for automating a synthetic biology workflowPrem Prakash Singh
- Improvements for Newt, a Cytoscape.js based SBGN editorAhmet Çandıroğlu
- PathwayMapper Improvements and Integration into cBioPortalKaan Sancak
- App Store for Cytoscape AppsSarthak Srivastava
- Simulating systems biology models in JavaShalin
- GraphSpace: Git for graphsDaniyal
- Upgrading Ontology Tagging at WikiPathwaysDara Akdag
- Rendering Complex Genetic Design with DNAplotlib for a Beautiful Visualization of Genetic CircuitSunwoo Kang
2017
20 acceptedShow
- Interconversion of the SBML and SBGN Modelling Languages using Semantics of LogicHaoran Yu
- Cytoscape.js Extension for Querying Large NetworksHasan Balcı
- Extending the IBW Biocompilation Interface with SBOL and SBML Import/Export Capabilitiesbodun
- PiType: A Protein Interaction Prediction Cytoscape AppMWrana
- Improvements in Tool for Curating Biological Maps in SBGNIlkin Safarli
- OpenGL-accelerated Renderer for Cytoscape 3MENGHE ZHANG
- WikiPathways Pathway Presenterjcbwndsr
- Implement Network Quantity Information measure in CentiScaPe #64Ivan Bestvina
- libGPML library to read and write GPML filesSaurabh Kumar
- Develop a web service which provides simulation / steady state analysis / parameter estimation with SBML modelsTakahiro Yamada
- Notification system for GraphSpaceMelvin Mathew
- Developing a web interface for DoMo-PredLong Zhang
- Developing a Cluster Computing Framework for Dynamical ModelingShaik Asifullah
- Implement GeneMANIA in Julia for High-performance ComputingGuodong Xu
- Roadmap to create a WebApp for the Enrichment Map Using Cytoscape and RESTful servicesBhavesh Narra
- Implementation of a Python Library for GraphSpace RESTful APIsSandeep Mahapatra
- Develop a Synthetic Biology Publication Workflow that Leverages the Synthetic Biology Open LanguageZach Zundel
- Adding support for PSIMI-TAB format to the Disease Variant Impact (DV-IMPACT) DatabaseRaghav Jajodia
- cyTRON: a Cytoscape app for the visualization of evolutionary trajectories in cancer progressionEdoardo Galimberti
- Cytoscape app for GraphSpace (CyGraphSpace)Rishabh Sethi
2016
15 acceptedShow
- Principal Coordinate Analysis and t-Distributed Stochastic Neighbor Embedding in clusterMaker2Supun Arunoda
- Enhance vignettes and plugin use for R package RCy3 for network manipulation using Cytoscapejooolia
- Visualizing genomic alterations in TCGA cancer pathways in cBioPortalIstemi Bahceci
- Improving Web Based SBGN Editor SBGNViz.jsMetin Can Siper
- Java support for Deviser, a code generation system for SBML librariesHovakim Grabski
- Import graphs in multiple formats and Cytoscape files into GraphSpaceMridulS
- GSoC: JSBML Validation SystemRoman Schulte
- SBGN-ML and SBML to Escher ConverterDevesh Khandelwal
- Interconvertible Layout program for CellDesignerKaito
- Interconversion between the systems biology modeling formats SBML and BioPAXtramy
- Multithread Centiscape (#55)ibestvina
- Cytoscape command line scripting enhancementsAshish Tiwari
- The Online Resource for Interface Based Interaction Networks (TOR-IBIN) Web InterfaceMilesGSOC
- Tutorials for Cytoscape.jsjoseph.stahl
- Extending Cytoscape.js: Addition of Clustering AlgorithmsZhaoyuan Zoe Xi
Public proposals
2- NRNB proposal by Pankaj Yadav2021 · Pankaj Yadav · Accepted · from COPS-IITBHU/GSoC-Accepted-Proposals
- Sankha Das - SBML4Humans - Interactive SBML Report for Humans2021 · Status not recorded · from Google-Summer-of-Code-Archive/gsoc-proposals-archive
Read them for structure, not to copy. All proposals for National Resource for Network Biology (NRNB).
