Improvement of MPBioPath for Reactome Scale Perturbation Analysis
Contributor: Chryseis Xinyi Liu
MP-BioPath uses rigorous mathematical programming to predict exactly how genetic mutations or drug perturbations cascade through Reactome's...
Science and medicine
Open Genome Informatics
Open access genomics and bioinformatics projects
Technologies
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Topics
bioinformaticsbiologyclouddata discoverygenomics
- Total projects
- 31
- Years participating
- 7
- Most recent
- 2026
Participation history
Historical projects
AI System for Real-Time Detection of Pediatric ENT Health Trends on Social Media
Contributor: M4x
Parents and caregivers increasingly turn to social media for pediatric ENT advice, where misinformation about conditions like ear infections and...
Patient-Facing Clinical Trial Chatbot with Interactive Map
Contributor: Mohamed Amine Haouas
Cancer patients navigating clinical trial databases face complex search interfaces with dozens of technical filters, making it difficult to find...
Improved Continuous Integration for Reactome
Contributor: sskrishn
Currently, at the Ontario Institute of Cancer Research, Jenkins is being used to run the release pipelines and this project proposes moving the...
Community Access Portal to Reactome Archive
Contributor: Asanka
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...
Implementing and Visualizing MP-BioPath tool in the FI Viz Cytoscape Plugin
Contributor: ModeEric
This project entails the creation of the MP-BioPath tool into the FI Viz Cytoscape Plugin. Biological pathways model the set of actions that...
Reactome Pathway Embeddings
Contributor: Lovro Vrcek
In the last several years, deep learning became widely used in various different fields, ranging from object detection and face recognition to speech...
Visualization Of Systems-Level Gene Annotation (UI-Side)
Contributor: Lokesh Rana
This GSoC project proposes to create the UI side of a network-based hierarchical viewer to visualize gene annotation at various levels of systems...
Interactive viewer for systems-biology variant interpretation (Server-side)
Contributor: Rishabh kohale
Genomic assays generate lists of genes or proteins statistically associated with a condition, such as being altered in disease. Genes need to be...
Bioinformatics with Jupyter Notebooks
Contributor: Prajna
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...
Authentication and Authorization Service for the Alliance of Genome Resources
Contributor: Aoji Xie
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...
Single-Cell pathway annotation pipeline
Contributor: Joao Luiz
Single-Cell sequencing is a new methodology that provides high-resolution data to understand individual cells. Applied to RNA sequencing, it can...
JBrowse 2 - Ensembl VEP integration
Contributor: Andra Vasilache
This project aims to integrate Ensembl VEP into the developing JBrowse 2. For this to happen, every component feature of this project must be...
Query Reactome Data in R
Contributor: Chi Lam Poon
R has been extensively used in bioinformatics research. However, there is still no direct way to obtain Reactome’s information in R. This project...
Phylogenetic tree viewer for JBrowse 2
Contributor: Shreya Srivastava
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...
GraphQL Interface For Querying Reactome Data
Contributor: Pratik Lodha
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...
Building functional and performant DataTable for WormBase
Contributor: Hitonari Sato
WormBase is a comprehensive research knowledge base on the genetics, genomics and biology of C. elegans and related nematodes. Biologists access...
InterMine Registry
Contributor: Leonardo Kuffo
The InterMine Registry will allow users to obtain and search, by consuming a RESTful API, basic information about existing InterMine instances. This...
Development of a Statistical Framework to Identify Similar Nodes in InterMine
Contributor: Samyadeep Basu
InterMine is a large graph containing entities(Genes, Transcription Factors etc. ) with important relationships between them. The main aim of the...
Prototype a new RESTful API querying Neo4j database
Contributor: yasharmaster
Description InterMine is an open source data warehouse which is used to store complex biological data. It is currently using PostgreSQL as the...
Stand-alone Reactome server in a Docker image
Contributor: Ayushya Chitransh
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....
Expansion of functionality and creation of detailed and exciting bioinformatics R demos for InterMineR package
Contributor: Konstantinos Kyritsis
InterMine constitutes a data warehouse framework, which provides the ability to access, retrieve and analyze rapidly a variety of biological data...
iOS InterMine app
Contributor: Nadezda Yudina
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...
Performance and user-centric upgrade to Afra
Contributor: aniarya82
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...
Pan-Genome Module for the Genome Context Viewer
Contributor: Alan Cleary
With the number of sequenced and annotated genomes continuously increasing, there is a need for new algorithms and tools for comparative analyses...
Interactive visualisation framework for genome mutations in gene and protein networks
Contributor: krassowski
I have wrote a set of thoughts expanding the original proposal "Interactive visualisation framework for genome mutations in gene and protein...
Using Go-Docker to enhance Galaxy functionalities
Contributor: Varun Shankar S
Go-Docker is a cluster management tool using Docker as execution/isolation system. It can be seen like Sun Grid Engine/Torque/… Using Bioinformatics...
Work with the Dockstore Team and the GA4GH to Enable Cross Docker Repository Sharing
Contributor: ulim
With the development of software container technology, developers can manage and deploy their software effectively. The software can start up and run...
Lightweight chat plugin for the JBrowse genome browser
Contributor: Pubudu Dodangoda
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...
Biological Graph Visualizations
Contributor: Samyadeep Basu
The proposed project deals with the development of two Drupal modules, for storage and visualizations of Complex Biological Graph. Both the proposed...
Visualisation for BLAST results
Contributor: aniarya
Build a Standalone library / tool to visualise the BLAST results. This tool will be build on Ruby as command line tool. Types of visualisation ...