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Science and medicine

Global Alliance for Genomics and Health

We develop genomics tools to benefit human health

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Participation history

10 GSoC years

2026202420232022202120202019201820172016

2026

4 projects

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GA4GH ServiceInfo Sidecar

The GA4GH Service Info API is a required component across standards such as TES, WES, and TRS, providing essential metadata about a service....

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Workflow Clinic

Thousands of bioinformatics workflows registered on public platforms like Dockstore and WorkflowHub cannot run on modern cloud platforms. Not because...

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RegBot LLM Compliance Assistant Genomics

Genomic data sharing is slowed by manually cross-checking consent and data-use language against dense GA4GH and related policy text, while generic...

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GA4GH-aligned Trustworthy Federated AI

This proposal addresses the deployment gap in federated learning for genomics, where frameworks like FLAN enable distributed model training but lack...

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2024

5 projects

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Python library for packaging and reusing Cloud Computing workload traces

The goal of this proposal is to address the issue of how difficult it can be to package and reuse computational workflows and analyses in genomics...

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Crypt4GH Support for GA4GH Task Execution Service API Implementations

Crypt4GH is a file format developed by GA4GH that keeps genomic data encrypted at rest and in transit. Currently, implementations of the TES API do...

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Extensible GA4GH Client Library/SDK and Command Line Interface implemented in Rust

This proposal aims to create a client library in rust and command line interface (CLI) for interacting with GA4GH environments in python. It will be...

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Dashboard Web Components (React, Vue etc) for file upload and handling

The project's objective is to create adaptable web components utilizing UI frameworks like LitElement. These components will adhere to the Data...

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TESK - A GA4GH-TES based Kubernetes batch execution service

This project endeavors to revamp the Kubernetes batch execution service to adhere to the Task Execution Service (TES) standards established by the...

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2023

7 projects

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GA4GH-FHIR Molecular Consequence Harmonization

The Proposal is how to make updates in the reference implementation based on the harmonization work, the creation of the new FHIR profile, and the...

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Web Components for discovering and using scientific software in the Cloud

The Global Alliance for Genomics and Health (GA4GH) defines the Tool Registry Service (TRS) specification for the discovering and accessing research...

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Implementation of the Sequence collection specification using the EVA contig alias backend

This project aims at implementing the Sequence Collection specification designed by the Global Alliance for Genomics and Health (GA4GH). The main...

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Dashboard Web Components (React, Vue etc) for Workflow and Task Runs

The objective of this project is to create adaptable web components using UI frameworks like Microsoft's Fast. This will involve expanding the...

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Implementing Phenopackets in a Variant Discovery Pipeline

Variant filtration is key to rare disease discovery. For a rare disease discovery app to be successful, it must be able to cleanly represent the...

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Common compliance testing framework for every OpenAPI specification

An interoperable automated framework for compliance testing has been developed, equipped with the capability to execute customizable test files. The...

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Creating a reproducible VRS mapping and validation library for MaveDB

The aim of this project is to make it easier to use MaveDB datasets for clinical use, as most of the MaveDB datasets are not annotated in a way that...

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2022

8 projects

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GSoC Proposal Global Alliance for Genomics and Health [ Shubhrajyoti Dey ]

This proposal aims on solving a problem to create user customisable forms on pedigree data of patients and storing it as per the GA4GH Standards to...

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Compliance testing framework for the Task Execution Service API

Task Execution Service (TES) is a Global Alliance for Genomics and Health (GA4GH) standard that allows federating and distributing computing tasks...

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Multi-model approach for discovery of associations between gene variants and diseases.

To identify possible relations between gene variants, phenotypes, and diseases - an ideal way would be a multi-model approach that involves: •...

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BioSerDe: (De)Serializing bioinformatics file formats to alternative representations

The field of bioinformatics has used many different extensions to express genomics data throughout its history, most of them focusing on simplicity...

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Increasing Support for Molecular Consequence Data in Genomic Standards

Molecular consequences of genetic variants determine their impact. For example, the variant NM_001330311.2(DVL1):c.1594del is a frameshift variant...

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TES Callback endpoint and mechanism in TESK

The goal of this project is to implement a callback mechanism for task status updates in TES, which will send requests from the server to the client...

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Federating workflow execution using GA4GH Cloud APIs

The Task Execution Service (TES) API and the Workflow Execution Service (WES) are two of the several standards defined by the Global Alliance for...

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Dynamic computation of variant annotations using GA4GH Variant Annotations plus FHIR Genomics

This project aims to demonstrate sharing of annotated genomic variants between clinicians and knowledge bases using a clinical decision support (CDS)...

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2021

7 projects

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Brokering Continuous Delivery through the ELIXIR Cloud service registry

The solution will act as a BROKER that manages subscriptions for update notifications for each deployment subscribed by system administrators System...

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Pure Rust Htsget Implementation

The aim of this proposal is to build a pure Rust serverless implementation of htsget - a client/server protocol for reliably and securely sending...

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React diagram component library for creating pedigree drawings tools

Scope Project scope is to develop a React.js library of pedigree components that will meet the GA4GH standards. Library will be build of accessible...

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Implement TES in Galaxy/Pulsar

To increase the interoperability of the Galaxy Platform with GA4GH Cloud-compliant solutions, the goal of this project is to add support for the TES...

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Implement reusable GA4GH UI clients

This project is based on the idea of the simplest form of micro-frontends that we can provide our users with our services like Cloud Registry, TRS,...

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Pure Rust serverless htsget implementation

The goal of this proposal would be to implement the htsget protocol in pure Rust using the noodles crate. It also has the objective of making a...

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vcf2fhir for Structural Variants

vcf2fhir is a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration. The utility currently converts simple variants (SNVs,...

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2020

4 projects

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Web application for trait-to-ontology mapping

Mapping free text trait names to ontologies so that they can be processed is an important task that is not yet standardized. The goal of this project...

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JSON Schema Repository and Browser

JSON Schema is a vocabulary to specify the structure of a JSON document. JSON Schema is widely used and well supported and sees a growing use for...

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Dynamically adding data to DRS

Storing, sharing and accessing the vast volumes of data being generated in modern research and healthcare settings is extremely daunting. With the...

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Reference registry + contig alias search

Reference sequences are files that are used as a reference to describe variants that are present in analyzed sequences and play a central role in...

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2019

5 projects

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Task distribution logic for GA4GH Cloud APIs

The Global Alliance for Genomics and Health aims to provide end-to-end solutions for clinical data use cases. The sensitive nature of data in the...

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Data pipeline for exchange of genomic variation between public repositories

The main goal of this project is to implement a mechanism to be in sync with the latest human data submitted to dbSNP. Once imported, this...

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Data repository service

The Data Repository Service (DRS) API provides a generic interface to data repositories so data consumers, including workflow systems, can access...

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RESTful API for genomic variation search

The Beacon specification allows to query whether a genomic variation is present in a repository. But the current implementation is based on an...

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Generic compliance framework for GA4GH APIs

The aim of this project is to build a compliance framework, to ensure that all new implementations/products/APIs adhere to the central specification...

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2018

4 projects

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Connect genomic sample discovery and sequencing data streaming

BioSamples is the EMBL-EBI central hub for metadata about samples whose raw data is hosted in reference archives such as EGA, ENA and EVA. The goal...

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Reference Sequence Retrieval API

This proposal consists of the development of a compliance test suite for Reference API servers with validation and checks for URLs, status codes,...

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Simplify usage of VCF validation suite

vcf-validator is a suite of command-line tools that can validate and fix VCF files. The goal of my project is to overcome the limitations of the...

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Proposal: Global filesystem and search engine for genomics data

Data Object Service (DOS) is an emerging standard for specifying location of data across different cloud environments. The goal of DOS is to create a...

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2017

2 projects

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Improve Structural Variants Support in VCF Validator

The VCF (Variant Call Format) is a format for text files, which is generally stored in a compressed manner to make the data retrieval of variants...

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VCF Streaming API Server and Specification

“Htsget retrieval API spec” [1] is a specification by the Global Alliance for Genomics and Health (GA4GH) for genomics bulk data transfers. This is a...

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2016

3 projects

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GSoC Student Proposal for SMART/FHIR and GA4GH

I am submitting a proposal for integrating SMART/FHIR and GA4GH

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Beacon Compliance Suite

Main tasks include the following: the Beacon project and Beacon Networks project need a Java client to be implemented. The configurable clients...

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Building a Better Beacon: Developing Supporting Tools for the Beacon Project

With beacons being lit and the specification readily being adopted by organizations all over the world, there is a need for a toolkit which...

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