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Science and medicine

National Resource for Network Biology (NRNB)

Developing open source tools for network biology

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Participation history

11 GSoC years

20262025202420232022202120202019201820172016

2026

7 projects

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Implement a Data-Driven Visual Attribute Mapping System in GraphSpace

This project aims to implement a Visual Attribute Mapping System that enables users to automatically map node and edge attributes to visual...

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openPIP 2 Modernizing the Open Source Protein Interaction Platform

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 /...

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Enhancing VCell AI Platform

VCell-AI is an AI-powered platform for discovering, analyzing, and exploring biological models from the VCell database. While the platform already...

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Proposal for the Unified App Registry for Cytoscape App Store

Currently, the Cytoscape App Store only supports plugins for the Cytoscape Desktop App. Since a web version of Cytoscape is available, web plugins...

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Evaluating and Improving Symbolic Regression Methods for Biological Network Dynamics

This project aims to improve and evaluate symbolic regression methods for discovering interpretable mathematical models of biological network...

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ML Models that use SBOL for DNA annotation by Shreeya

Developing a scalable and reproducible research pipeline within SeqTrainer for bacterial DNA sequence modelling and annotation using SBOL-based...

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Direct Integration of PathVisio with WikiPathways GitHub

This project aims to develop a Direct GitHub Integration Plugin for PathVisio to transform the pathway curation workflow from outdated systems to the...

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2025

8 projects

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SBOL2 SBOL3 Convertor Utility

The Synthetic Biology Open Language (SBOL) serves as a vital community standard for representing biological designs, with version 3.1 offering mature...

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Developing a Highly Efficient Numerical ODE Solver in the Systems Biology Simulation Core Library

The field of computational biology depends significantly on mathematical modeling to simulate complex biological simulations, often involving...

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SeqTrainer - creating datasets from SynBioHub to aid researchers in creating machine learning models

In the realm of synthetic biology, there is a significant source of data in the form of models, genetic sequences, regulatory networks, and...

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CySBML Reloaded: Smarter, Simpler, Automated

CySBML Reloaded: Smarter, Simpler, Automated focuses on upgrading CySBML — a Cytoscape app for visualizing computational models encoded in SBML. The...

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Enhancing SBOannotator with LLM Integration & Dynamic Term Retrieval

This proposal aims to transform SBOannotator from a static, hard-coded tool into a dynamic, intelligent system for annotating SBML models with...

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VCell-AI: AI Analysis & Querying Platform

The VCell-AI Platform is an AI-powered system for discovering, analyzing, and exploring biomodels, publications, and research papers from the VCell...

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Enhancing the Systems Biology Simulation Core Library (SBSCL) with a Solver-Agnostic Framework...

This project addresses the current incompatibility of the Systems Biology Simulation Core Library (SBSCL) with modern computing architectures,...

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LLM-Powered Interactive Chat Interface for CellMinerCDB with GraphRAG Integration

This project will develop an intelligent chat interface for CellMinerCDB, a cancer genomics database, using GraphRAG (Graph Retrieval-Augmented...

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2024

11 projects

Official year page

GPML support in Newt

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...

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Machine Learning Support for Constructing Newt SBGN Maps

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...

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Integration of complexity score functions into the iGEM DNA kit distribution workflow

The goal is developing an updated workflow that uses the existing iGEM distribution structure to integrate a synthesizability assessment of genetic...

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ASCETIC Vision

This project aims to enhance the accessibility and usability of the ASCETIC framework, which interprets tumor evolutionary signatures crucial for...

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Integration of GRN inference algorithms using single cell multi-omics data to BEELINE

BEELINE is a bench marking tool that evaluates different methods and models that infer Gene Regulatory Networks (GRN) from Single cell gene...

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COBRAxy: COBRA and MaREA4Galaxy

MaREA4Galaxy is a user-friendly tool designed to facilitate the characterization and graphical comparison of sample groups exhibiting distinct...

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Implement AWS DevOps Pipeline for Image Deployment for Graphspace

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...

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Large Language Model-based creation of knowledge graph from a publication

This project proposes the development of a Python web application that utilizes Large Language Models (LLMs) for extracting, transforming, and...

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Using Foundation Model: scGPT for Gene Regulatory Network Inference

The project aims to develop a robust pipeline for assessing the performance of foundation models, specifically focusing on scGPT, in generating...

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Cytoscape layout plugin to support Cytoscape.js layouts

Cytoscape Desktop Application serves as a powerful tool for network analysis and visualization. However, its layout options are limited compared to...

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Improvement Of openPIP (Data upload & Visualization)

OpenPIP platform is typically necessary alongside a research paper detailing experimental data, alongside depositing the data into a standard...

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2023

8 projects

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Automate Cytoscape.js release process using GitHub Actions

Cytoscape.js is an open-source JavaScript-based graph theory library that can be used for graph analysis and visualisation. It contains many useful...

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Development of a Cytoscape App for microbe-microbe association networks

Microbial associations play a fundamental part in deciphering underlying mechanisms of microbial communities. A series of algorithms have been...

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Generate Example Dataset for PyTorch Geometric Based on Pathway Commons and Prototype

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...

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Supporting Pathway Commons and ssGSEA in clusterProfiler

clusterProfiler is an efficient package that provides a universal interface for gene functional annotation from a variety of resources and is...

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Develop new features for Cytoscape App-cyPlot

This project involves updating cyPlot(a Cytoscape app written in JAVA) which provides the ability to plot data through GUI or CyCommands/REST. CyPlot...

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Setting up the CI/CD Pipeline using Github Actions on GraphSpace

Currently the Graphspace code repository has a lot of mismatched dependency issues & consist no automating techniques in their repository to release...

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Convert CellBox Tensorflow code to Pytorch

CellBox is a model for predicting cell states under drug perturbations, whose code base was originally written in Tensorflow 1. Since Tensorflow 1...

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Implement a R Shiny module for Network Analysis in CellMinerCDB

CellMinerCDB provides a web-based resource for integrating multiple forms of pharmacological and genomic analyses, and unifying the richest cancer...

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2022

8 projects

Official year page

SBML-MINERVA support in Newt

Currently, the Newt editor supports Systems Biological Graphical Notation (SBGN) and Simple Interactive Format (SIF) formats while also allowing...

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Create a Pipeline from data extraction to execution of GNN based Drug Response Prediction

The use of machine learning models in medicine is expanding, but there are still undergoing due to the interpretability. One useful example which has...

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High-throughput simulation for computational cell biology with Cloud-COPASI

Customized SSH Authentication Free Implementation of the Cloud-COPASI for UConn users: The project proposal aims to create a customized version of...

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Updates to the Enrichment Table App

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...

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Adding visualization of protein-complex interaction to OpenPIP

OpenPIP (Open Source Protein Interaction Platform) is an open-source software package for hosting protein-protein interaction (PPI) data based on the...

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Conversion between GenBank and SBOL3

The SBOL-Utilities repository is a python library that provides many useful methods and utilities on top of the main PySBOL3 implementation of SBOL3....

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NetBoxR Updates

netboxr is an R package for the automated discovery of biological process modules by network analysis. The project involves updating netboxr...

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Create Jupyter Notebooks showcasing COMBINE Standards

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of various community standards and formats in...

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2021

13 projects

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Enhancing ABioTrans Plus using Gene Expression Omnibus database and adding analysis report

This project aims to add new features to ABioTrans Plus(GeneCloudOmics) that includes the direct import of gene expression data from Gene Expression...

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Simple Enrichment Tool for Analysis

Cytoscape is a highly popular open source bioinformatics software platform for visualizing, analyzing, and publishing graphs or networks representing...

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Develop a Cytoscape App for the Casual Path Algorithm

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...

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Enhancing the admin panel of openPIP

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...

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Local DB support for SBGN maps in Newt

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...

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Develop GUI for ImageJ groovy script calling VCell API

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...

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Expand ModelBricks.org and VCell API

ModelBricks is a tool for bioinformatics researchers that allows users to browse, view, and download detailed models of biological processes. I...

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SBML Simulator in Rust

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...

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Adding Multi-omics data support to ABioTrans Plus

ABioTrans Plus is a web server for transcriptome data analysis and visualization. It supports the analysis of microarray and RNASeq data and performs...

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PD to AF conversion facility in Newt

Newt supports the Process Description (PD) and the Activity Flow (AF) graphs of SBGN. However, there is no conversion between these two graphs in...

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SBML4Humans - Interactive SBML Report for Humans

Systems Biology Markup Language (SBML) is a standard format for the representation and exchange of biological models between computers. The...

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Implementing multiple clustering algorithms and dimensionality reduction techniques on clusterMaker2

Implementing following dimensionality reduction techniques and clustering algorithms to clusterMaker2: UMAP, t-SNE, PCA, PCoA, Louvain, Walktrap,...

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TumorComparer, updated version

TumorComparer, updated version The TumorComparer is a computational method for the comparison of different cancer types with cancer cell lines by...

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2020

15 projects

Official year page

Generating detailed SBOL representation of genetic logic circuits along with improved designing capability, and Java-Python conversion.

GeneTech allow users to develop genetic logic circuits only by specifying a Boolean function. The tool first performs Boolean optimisation, followed...

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Implementation of SBML-JSON converter and SBML-JSON scheme

The Systems Biology Markup Language (SBML) is the main language for representation and exchange of computational models in biology. JSON is the main...

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LACE-View : A Visualizer for Longitudinal Clonal Trees

LACEview is a visualization tool for LACE (Longitudnal Analysis of Cancer Evolution) developed by a team at BIMIB. The tool is for R visualization...

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Enhance Web Interface for Natural-Language Processing Extracted Interaction Network

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,...

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Developing a tool for implementing clustering algorithms to Cytoscape app ClusterMaker2

In this project, I will develop a tool in Cytoscape app ClusterMaker2 that helps implementing new clustering algorithms in the app from inside...

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Adding Bio-Statistical Machine Learning Models and Graphical visualization to ABioTrans V2

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...

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Development of a system that generates spatial SBML models using deep learning

This project aims at creating and implementing a system that automatically generates various spatial SBML models by comprehensively segmenting...

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Simulation of systems biology models in Java: support for new features

Systems biology studies the mechanisms underlying complex biological processes as integrated systems of many interacting components. Modeling...

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Redevelop Model Bricks code base architecture

Model Bricks project is an effort focused on describing recurring patterns in biological networks. These patterns are described as small VCell models...

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Implement a comment/discussion system in GraphSpace

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...

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Enhancing PathwayMapper in cBioPortal and PathwayMapper editor

Pathways are created by selecting certain genes and studies then displayed in the PathwayMapper tab in the cBioPortal. However, not every page in...

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Improving compmodelmatch.org

This project intends to make several improvements to compmodelmatch platform which will improve its performance and also add features such as ORCID...

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Integration of sequence visualization into SynBioHub

As a design repository for Synthetic Biology, SynBioHub facilitates the sharing and searching for information, combining data from a variety of...

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Integrating RRPlugins with libRoadRunner

LibRoadrunner is a high-performance SBML based simulator that uses LLVM to generate very efficient runtime code. This enables LibRoadrunner to...

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Spreadsheet Plug-in for SynBioHub

Synthetic Biology is a discipline that connects many disciplines and heterogeneous researchers. To be useful as a tool, a platform such as SynBioHub...

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2019

11 projects

Official year page

Implement a machine-readable graph legend interface

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...

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Integrating RRPlugins with libRoadRunner and devloping Differential Evolution optimizer plugin

LibRoadrunner is a high performance SBML based simulator that uses LLVM to generate very efficient runtime code. This enables LibRoadrunner to...

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Extending ModelPolisher to a universal model annotation tool

ModelPolisher is a model annotation tool for the BiGG Models Knowledgebase. Annotations enhance the reusability and interoperability of biological...

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

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...

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New Build System for InSilico

InSilico is an extensible editor which can be used for manipulating and analyzing many different file types, SBML files in particular. The current...

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Simulator for Systems Biology

Develop a simulator which will support all the features of SBML core specification Implement a code so that the simulator can pass testcases which...

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Web Interface for NLP Extracted Interaction Network

An application for users to access biological data extracted from biomedical literature. Project Mentor Augustin Luna Objectives Easy search...

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Validation of spatial systems biology models in Java

The spatial extension for SBML provides support for describing processes that involve a spatial component. This project seeks to implement validation...

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App Store for Cytoscape Apps

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...

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BridgeDb Major Release

BridgeDb is a platform used for identifier mapping in WikiPathways and PathVisio with support for various languages like as a Cytoscape plugin, as an...

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GraphSpace: Diffs for graphs

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...

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2018

10 projects

Official year page

Develop cyTRON/JS: a backend and a cytoscape.js visualizer for cancer progression models

This project aims at developing a tool which should provide an interactive visualization of the cancer progression models produced by the R library...

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Implement SBML Array Support in libRoadRunner

LibRoadrunner is a high-performance SBML based simulator for Systems and Synthetic Biology that uses LLVM to generate very efficient runtime code....

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Integrating CAD and CAM tools for automating a synthetic biology workflow

Integrated Build Software Optimisation Tools (BOOST) with SBOLDesigner. SBOLDesigner is a CAD tool for creating and manipulating the sequences of...

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Improvements for Newt, a Cytoscape.js based SBGN editor

Newt is a free, web-based, open source viewer and editor for pathways in Systems Biological Graphical Notation (SBGN). It is written with a series of...

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PathwayMapper Improvements and Integration into cBioPortal

While the network visualization module in cBioPortal is a powerful exploration tool, most biologists are more comfortable with the kind of...

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App Store for Cytoscape Apps

The project is “Appstore for the CytoScape Apps” with Alex Pico, Barry Demchak and Scooter Morris as its mentor. The goals for the summer will be to...

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Simulating systems biology models in Java

Computational models of biological systems play an important role in advancing science as they give insights about the biology without the need for...

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GraphSpace: Git for graphs

GraphSpace is a web-based platform where collaborating research groups can use a user-friendly interface to create, interact and share networks....

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Upgrading Ontology Tagging at WikiPathways

Ontologies are an integral part of our scientific progress. The ability to share common definitions is crucial to answering questions, thus, an...

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Rendering Complex Genetic Design with DNAplotlib for a Beautiful Visualization of Genetic Circuit

Visualizing genetic circuits is essential in the field of synthetic biology. These genetic designs often involve complex representation of modular...

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2017

20 projects

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Interconversion of the SBML and SBGN Modelling Languages using Semantics of Logic

Systems biology researchers study the network of molecular interactions within a biological system and publish the deduced models in a diagram...

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Cytoscape.js Extension for Querying Large Networks

Traversal-based graph algorithms are good at extracting “subgraphs of interest” when applied to large networks. However, applying known algorithms...

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Extending the IBW Biocompilation Interface with SBOL and SBML Import/Export Capabilities

The Infobiotics Workbench (IBW) is a synthetic biology design tool with three major functionalities: stochastic simulations, which mimic the...

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PiType: A Protein Interaction Prediction Cytoscape App

PiType is an already existing protein-protein interaction classifying tool created by my mentor. It currently exists as both a web app and a...

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Improvements in Tool for Curating Biological Maps in SBGN

SBGNViz is a Cytoscape.js based library for viewing biological maps in Systems Biology Graphical Notation (SBGN) notation. ChiSE is a library based...

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OpenGL-accelerated Renderer for Cytoscape 3

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways. It integrates these networks...

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WikiPathways Pathway Presenter

WikiPathways is an open and collaborative platform for sharing biological pathway information. It features an interactive diagram that aids the user...

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Implement Network Quantity Information measure in CentiScaPe #64

CentiScaPe is a Cytoscape application used to calculate a number of different node centralities of an optionally weighted network, both directed and...

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libGPML library to read and write GPML files

libGPML Currently it is required to include the whole PathVisio core module which is much bigger and already contains PathVisio specific...

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Develop a web service which provides simulation / steady state analysis / parameter estimation with SBML models

In systems biology, it is very important to formalize the model for biological phenomenon and analyze based on this model basically constructed by...

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Notification system for GraphSpace

GraphSpace is an user-friendly web-based platform that collaborating research groups can utilize for storage, interaction, and network sharing. A...

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Developing a web interface for DoMo-Pred

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...

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Developing a Cluster Computing Framework for Dynamical Modeling

Integrating the existing Tellurium project with Apache Spark and by which the computations or simulations can be run in parallel. Developing an API...

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Implement GeneMANIA in Julia for High-performance Computing

The aim of the project is to Implement GeneMANIA in Julia to optimize netDx for high-performance computing. The current Java-based implementation of...

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Roadmap to create a WebApp for the Enrichment Map Using Cytoscape and RESTful services

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...

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Implementation of a Python Library for GraphSpace RESTful APIs

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...

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Develop a Synthetic Biology Publication Workflow that Leverages the Synthetic Biology Open Language

A large goal of both the SBOL and synthetic biology communities is to develop a useful and comprehensive workflow from experiment to publication....

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Adding support for PSIMI-TAB format to the Disease Variant Impact (DV-IMPACT) Database

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...

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cyTRON: a Cytoscape app for the visualization of evolutionary trajectories in cancer progression

TRONCO is an R package that implements state-of-the-art algorithms for the inference of cancer progressions with the ultimate goal of understanding...

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Cytoscape app for GraphSpace (CyGraphSpace)

The overall goal of the project is to create a Cytoscape app (CyGraphSpace) for syncing networks from Cytoscape to GraphSpace and vice-versa....

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2016

15 projects

Official year page

Principal Coordinate Analysis and t-Distributed Stochastic Neighbor Embedding in clusterMaker2

Implement two algorithms which have the ability to do dimensional reduction in cluster Network. Principal Coordinate Analysis and t-Distributed...

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Enhance vignettes and plugin use for R package RCy3 for network manipulation using Cytoscape

Many scientists use networks to visualize complex relationships among species, people, cities, genes, proteins or other subjects. Cytoscape is...

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Visualizing genomic alterations in TCGA cancer pathways in cBioPortal

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...

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Improving Web Based SBGN Editor SBGNViz.js

SBGNViz.js is an open source web application based on Cytoscape.js to visualize the pathway models represented by SBGN Process Description Notation ....

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Java support for Deviser, a code generation system for SBML libraries

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...

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Import graphs in multiple formats and Cytoscape files into GraphSpace

GraphSpace is a tool for storing, sharing, and visualising graphs in order to help collaborative research. Users can upload graphs and share it with...

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GSoC: JSBML Validation System

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...

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SBGN-ML and SBML to Escher Converter

Escher is quickly growing in popularity. As Escher currently uses JSON as its data and layout representation format, and most of the community...

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Interconvertible Layout program for CellDesigner

CellDesigner is a modeling/simulating software capable of visualizing, modeling, and simulating gene­regulatory and biochemical networks. The key...

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Interconversion between the systems biology modeling formats SBML and BioPAX

In the systems biology field, there exists many different standards, with each standard serving for a different purpose. BioPax is a standard used...

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Multithread Centiscape (#55)

CentiScaPe is a Cytoscape application used to calculate a number of different node centralities in a network. All of the centrality calculating...

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Cytoscape command line scripting enhancements

Cytoscape is a general purpose, open source software platform for complex network data integration, analysis and visualization. Cytoscape’s core...

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The Online Resource for Interface Based Interaction Networks (TOR-IBIN) Web Interface

TOR-IBIN will be an online resource for gathering and storing published interface-based protein-protein interactions (PPI). TOR-IBIN aims to make...

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Tutorials for Cytoscape.js

Tutorials serve as an invaluable way to familiarize oneself with new software. Cytoscape.js currently provides demos but lacks tutorials to tie...

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Extending Cytoscape.js: Addition of Clustering Algorithms

Cytoscape.js is a graph theory and networks library focused on providing built-in, rich and performant graph models for analysis and data...

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