Science and medicine

Open Genome Informatics

Open access genomics and bioinformatics projects

databasefrontendgraphjavascriptmysqlpythonrreactangular

Organization website

Participation history

7 GSoC years

2026 2023 2022 2021 2020 2017 2016

2026

3 projects

Official year page

Improvement of MPBioPath for Reactome Scale Perturbation Analysis

MP-BioPath uses rigorous mathematical programming to predict exactly how genetic mutations or drug perturbations cascade through Reactome's...

Project page

AI System for Real-Time Detection of Pediatric ENT Health Trends on Social Media

Parents and caregivers increasingly turn to social media for pediatric ENT advice, where misinformation about conditions like ear infections and...

Project page

Patient-Facing Clinical Trial Chatbot with Interactive Map

Cancer patients navigating clinical trial databases face complex search interfaces with dozens of technical filters, making it difficult to find...

Project page

2023

1 project

Official year page

Improved Continuous Integration for Reactome

Currently, at the Ontario Institute of Cancer Research, Jenkins is being used to run the release pipelines and this project proposes moving the...

Code Project page

2022

2 projects

Official year page

Community Access Portal to Reactome Archive

In Reactome, once the new data is released, preceding data will be archived in an AWS S3 bucket. Now they don't have a web interface for users to...

Code Project page

Implementing and Visualizing MP-BioPath tool in the FI Viz Cytoscape Plugin

This project entails the creation of the MP-BioPath tool into the FI Viz Cytoscape Plugin. Biological pathways model the set of actions that...

Code Project page

2021

6 projects

Official year page

Reactome Pathway Embeddings

In the last several years, deep learning became widely used in various different fields, ranging from object detection and face recognition to speech...

Code Project page

Visualization Of Systems-Level Gene Annotation (UI-Side)

This GSoC project proposes to create the UI side of a network-based hierarchical viewer to visualize gene annotation at various levels of systems...

Code Project page

Interactive viewer for systems-biology variant interpretation (Server-side)

Genomic assays generate lists of genes or proteins statistically associated with a condition, such as being altered in disease. Genes need to be...

Code Project page

Bioinformatics with Jupyter Notebooks

For an open-source tool for bioinformatics like WormBase, it is essential to have thorough documentation of features and use cases. As part of this...

Code Project page

Authentication and Authorization Service for the Alliance of Genome Resources

The Alliance of Genome Resources is a consortium of 6 model organism databases (MODs) and the Gene Ontology (GO) Consortium whose goal is to provide...

Code Project page

Single-Cell pathway annotation pipeline

Single-Cell sequencing is a new methodology that provides high-resolution data to understand individual cells. Applied to RNA sequencing, it can...

Code Project page

2020

5 projects

Official year page

JBrowse 2 - Ensembl VEP integration

This project aims to integrate Ensembl VEP into the developing JBrowse 2. For this to happen, every component feature of this project must be...

Code Project page

Query Reactome Data in R

R has been extensively used in bioinformatics research. However, there is still no direct way to obtain Reactome’s information in R. This project...

Code Project page

Phylogenetic tree viewer for JBrowse 2

It is a Phylogenetic tree viewer for the JBrowse 2 in the most dynamic way possible. With the help of Reactjs, it will be much more efficient than...

Code Project page

GraphQL Interface For Querying Reactome Data

Reactome currently uses a REST-based API that allows end-users to obtain specific data from a set of predefined end-points. To provide better...

Code Project page

Building functional and performant DataTable for WormBase

WormBase is a comprehensive research knowledge base on the genetics, genomics and biology of C. elegans and related nematodes. Biologists access...

Code Project page

2017

8 projects

Official year page

InterMine Registry

The InterMine Registry will allow users to obtain and search, by consuming a RESTful API, basic information about existing InterMine instances. This...

Code Project page

Development of a Statistical Framework to Identify Similar Nodes in InterMine

InterMine is a large graph containing entities(Genes, Transcription Factors etc. ) with important relationships between them. The main aim of the...

Code Project page

Prototype a new RESTful API querying Neo4j database

Description InterMine is an open source data warehouse which is used to store complex biological data. It is currently using PostgreSQL as the...

Code Project page

Stand-alone Reactome server in a Docker image

The goal of this project is to produce a Docker image that contains everything that an end-user needs to run Reactome on his/her own workstation....

Code Project page

Expansion of functionality and creation of detailed and exciting bioinformatics R demos for InterMineR package

InterMine constitutes a data warehouse framework, which provides the ability to access, retrieve and analyze rapidly a variety of biological data...

Code Project page

iOS InterMine app

InterMine has an Android application and is looking to make it available on iOS as well. Native iOS application will allow researchers to have access...

Code Project page

Performance and user-centric upgrade to Afra

The primary goal of the project is to upgrade Afra's annotation editing code, to provide it performance upgrade. Afra's annotation editor is built...

Code Project page

Pan-Genome Module for the Genome Context Viewer

With the number of sequenced and annotated genomes continuously increasing, there is a need for new algorithms and tools for comparative analyses...

Code Project page

2016

6 projects

Official year page

Interactive visualisation framework for genome mutations in gene and protein networks

I have wrote a set of thoughts expanding the original proposal "Interactive visualisation framework for genome mutations in gene and protein...

Code Project page

Using Go-Docker to enhance Galaxy functionalities

Go-Docker is a cluster management tool using Docker as execution/isolation system. It can be seen like Sun Grid Engine/Torque/… Using Bioinformatics...

Code Project page

Work with the Dockstore Team and the GA4GH to Enable Cross Docker Repository Sharing

With the development of software container technology, developers can manage and deploy their software effectively. The software can start up and run...

Code Project page

Lightweight chat plugin for the JBrowse genome browser

This project will deliver a lightweight socializing plugin for JBrowse using OAuth2 and the Faye pub/sub framework. Users will be able to chat, share...

Code Project page

Biological Graph Visualizations

The proposed project deals with the development of two Drupal modules, for storage and visualizations of Complex Biological Graph. Both the proposed...

Code Project page

Visualisation for BLAST results

Build a Standalone library / tool to visualise the BLAST results. This tool will be build on Ruby as command line tool. Types of visualisation ...

Code Project page