Implementations

Browse implementations of GA4GH products. Learn how they solve real problems for organisations around the world.

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All of Us Researcher Workbench

The Researcher Workbench is a cloud-based platform where registered researchers can access Registered and Controlled Tier data. Its powerful tools support data analysis and collaboration. Integrated help and educational resources are provided through the Workbench User Support Hub.

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ARGO Data Platform

The International Cancer Genome Consortium Accelerating Research in Genomic Oncology (ICGC ARGO) aims to uniformly analyse specimens from 100,000 donors with high-quality clinical data in order to address outstanding questions that are vital to the quest to defeat cancer.

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Australian Genomics Data Management Systems

Now concluded, Australian Genomics had tools to support storage, access, and sharing of its genomic datasets for secondary research use. They included a web-based platform for dynamic consent and data sharing preferences (CTRL), a cloud-based Genomic Data Repository (GDR) that ingested, stored, and provided access to data, and a data release coordinator system (Elsa) to streamline data sharing.

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BioBank Japan (BBJ)

BBJ is of the three major biobanks in Japan managed by the AMED BioBank Japan Project for Genomic and Clinical Research. It has collected DNA, serum, and clinical information from more than 270,000 patients nationwide, and thus is regarded as one of the largest disease biobanks in the world.

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Biomedical Research Hub (BRH)

BRH is an international cloud-based federated system for managing, analysing, and sharing patient data for research purposes, while allowing each separate resource to operate their component based upon their own governance rules and data structure.

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BRCA Exchange

Information drawn from multiple databases — which have been intelligently merged together — provides researchers with a set of BRCA variations and annotations that is as comprehensive as possible.

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CanDIG V2

The CanDIG v2 project is a collection of heterogeneous services designed to work together to facilitate end-to-end data flow for genomic data.

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ClinGen Knowledge-base

Funded by the National Institutes of Health (NIH), ClinGen is dedicated to building a central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.

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cwl-WES

cwl-WES (formerly: WES-ELIXIR) is a Flask/Gunicorn application that makes use of Connexion to implement the GA4GH WES OpenAPI specification. cwl-WES enables clients and users to execute CWL workflows in the cloud via an execution backend that is compatible with the GA4GH Task Execution Service (TES) — for example, TESK or Funnel. Workflows can be sent for execution, previous runs can be listed, and the status and run information of individual runs can be queried. The service leverages cwl-tes to interpret CWL workflows, break them down into individual tasks, and emit GA4GH TES-compatible HTTP requests to a configured TES instance. Access to endpoints can be configured to require JSON Web Token-based access tokens, such as those issued by ELIXIR AAI. Run information is stored in a MongoDB database.

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EJP-RD Beacon-in-a-Box

This stand-alone Beacon instance was designed to allow for the sharing of metadata of datasets.

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EJP-RD Virtual Platform

The platform is a federated ecosystem in which resources are enhanced to be amenable to rare disease research, and made FAIR: findable, accessible, interoperable, and reusable. Data stay at the source level but can be queried remotely. As an ecosystem, multiple query points will be possible, allowing for sending interrogations from one resource to others. Thus, federated discovery, query, and analysis are made possible, preserving patient privacy and respecting access conditions of each resource.

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ELIXIR BioContainers

BioContainers is based on the popular frameworks Conda, Docker, and Singularity. This community-driven project provides the infrastructure and basic guidelines to create, manage, and distribute bioinformatics packages (e.g Conda) and containers (e.g Docker, Singularity).

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ELIXIR Cloud & AAI

A multi-cloud computing infrastructure allows life scientists within and beyond the ELIXIR network to run large-scale data analysis workloads in a federated network of ELIXIR compute and storage nodes.

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ELIXIR European Genome-phenome Archive (EGA)

The European Genome-phenome Archive (EGA) is a service for permanent archiving and sharing of personally-identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems.

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ELIXIR-Beacon

The Beacon Network search bar is a simple form with two options: assembly and variant. The assembly can be selected from the dropdown menu on the left side. The search bar then takes the desired variant information as a search term which will be sent to Beacons in a structured manner.

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ENCODE RNAExpression report

This ENCODE Portal hosts data produced by members of the Encyclopedia of DNA Elements (ENCODE) Consortium and also provides the wider scientific community with access to these data.

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EpiShare Platform

The EpiShare Platform builds GA4GH tools and standards and other online resources. It aims to create a web resource to make epigenomic data more easily discoverable and to enable the launch of multi-omics analyses on these controlled-access datasets at their storage locations.

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Federated EGA

The Federated EGA provides a network of connected resources to enable transnational discovery of and access to human data for research while also respecting jurisdictional data protection regulations. By providing a solution to emerging challenges around secure and efficient management of human "omics" and associated data, the Federated EGA fosters data reuse, enables reproducibility, and accelerates biomedical research.

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Funnel

Funnel is a toolkit for distributed task execution via a simple, standard API.

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GA4GH TES on Azure

This implementation of the GA4GH TES API provides distributed batch task execution on Microsoft Azure.

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Genomics England Research Environment

The secure Research Environment provides approved researchers with a range of open source tools, shared storage drives, databases, and research platforms linking genomic data to a rich set of clinical, phenotypic, and longitudinal data.

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GTEx RNAget

This is an implementation of GA4GH's RNAget API for the Genotype Tissue Expression Project (GTEx).

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H3ABionet

H3ABioNet is a pan-African bioinformatics network for the Human Heredity and Health in Africa (H3Africa) consortium.

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Human Cell Atlas (HCA) Data Portal

The HCA Data Portal stores and provides single-cell data contributed by labs around the world. Anyone can contribute data, find data, or access community tools and applications.

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Life Science AAI

The Life Science Login enables researchers to use their home organisation credentials or community or other identities (e.g. Google, Linkedin, LS ID) to sign in and access data and services they need. It also allows service providers (both in academia and industry) to control and manage access rights of their users and create different access levels for research groups or international projects.

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Medical Genomics Japan Variant Database (MGeND)

Medical Genomics Japan Variant Database (MGeND) aims to provide integrated information about genomic variations and clinical characteristics, and improve clinical interpretation by cross-sectional studies on cancer, rare/intractable disease, infectious disease, dementia, and hearing loss. This database contains genetic variations and their frequencies with supporting evidence and clinical information that have been provided from research institutions and cooperating hospitals, which were selected for the Integrated Database of Clinical and Genomic Information programme supported by the Japan Agency for Medical Research and Development (AMED).

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MSSNG Genetics Application System

MSSNG (pronounced “missing”) is a groundbreaking collaboration between Autism Speaks, Verily, DNAstack, Hospital for Sick Children (SickKids), and the research community to create the world’s largest whole-genome-sequencing database on autism with deep phenotyping.

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National Genomic Information System (NGIS)

NGIS provides systems to enable the full end-to-end path from test ordering to interpretation and reporting for the whole-genome-sequencing component of the Genomic Medicine Service for England.

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NCI Data Commons Framework

The vision of the Data Commons Framework is to make it easier to develop, operate, and interoperate data commons, data clouds, knowledge-bases, and other resources for managing, analysing, and sharing research data that can be part of a large data commons ecosystem.

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NCPI Interoperability Projects and partners

The NIH Cloud Platform Interoperability (NCPI) effort aims to facilitate data availability by encouraging the adoption of common technical standards across various cloud platforms. This approach will enable researchers to conveniently access data from multiple platforms using a single sign-on system, streamlining the processes of data discovery, access, and analysis. NCPI works with partners to pilot and adopt GA4GH standards for data access, portable analysis workflows and tools, authorisation, and interoperability. The “Interoperability Projects” use cases are real-world examples from within the U.S. National Institutes of Health and partner organisations.

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NHLBI BioData Catalyst® (BDC)

BDC is a cloud-based ecosystem providing tools, applications, and workflows in secure workspaces that increases access to U.S. National Heart, Lung, and Blood Institute (NHLBI) funded datasets and innovative data analysis capabilities.

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NHLBI TOPMed BioData Catalyst

This is a full implementation of the DRS v1.1 standard with support for persistent identifiers. The open-source DRS server follows the Gen3 implementation. Gen3 is a GA4GH-compliant, open-source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org

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Omics AI

Omics AI is a modular software suite by DNAstack for driving insights from omics and health data networks. It has several components. Publisher is a tool for connecting, protecting, and sharing omics data. Explorer is a portal that makes it easy to find, access, and analyse data within and across organisations. Workbench enables users to perform omics data analysis in their own environment. Examples of public deployments of Omics AI include Neuroscience AI (neuroscience.ai), a data network powered by this software suite that was established by the Autism Sharing Initiative Driver Project. The portal makes it easy for researchers to discover, access, and analyse data neuroscience data collections. Similarly, Viral AI (viral.ai) makes it easy to discover, access, and analyse publicly available viral data collections.

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TESK

This is an implementation of a task execution engine based on the TES standard, running on Kubernetes.

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The Exomiser

The Exomiser is a Java program that functionally annotates variants from whole-exome-sequencing data in VCF v4.0 format. The functional annotation is performed with Jannovar and uses UCSC KnownGene transcript definitions and hg19 genomic coordinates.

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TogoVar

TogoVar is a comprehensive Japanese genetic variation database that has collected and organised genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them.

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Tohoku Medical Megabank Project (ToMMo)

The project conducts a long-term health study of 150,000 residents living in communities which suffered major damage from the Great East Japan Earthquake and reports the findings to the respective residents with their personal information. It also establishes a system of dispatching physicians on a rotation basis to healthcare providers in the region.

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Variant Interpretation for Cancer Consortium (VICC) Meta-Knowledgebase (v1)

This search interface for cancer variant interpretations is assembled by aggregating and harmonising across multiple cancer variant interpretation knowledge-bases.

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