What Technologies Do We Use?
Diagram outlining technologies used for Open Targets Genetics
Phase 1 of the pipeline is to prepare the input data (V2D, V2G and summary statistics tables) in a standardised way. Workflows are written in Python and run using Snakemake workflow management system to ensure analyses are reproducible and portable. Workflows are run on on a Google Compute instance, or the Sanger Institute cluster, and the output is stored on Google Cloud Storage (GCS).
Phase 2 of the pipeline processes and merges the input data to produce evidence linking traits to variants to genes. This merging pipeline is written in Scala and Spark running on a Google Dataproc cluster, which automatically scales to accommodate the quantity of the data. The output tables are saved in JSON files streamed directly to a Google Cloud Storage bucket before being loaded into a ClickHouse database.
The infrastructure used to serve the data through the front-end by an API runs on Google Cloud. It allows to elastically accommodate the unpredictable demand for usage at a global-scale and to keep DevOps operations at minimum levels. Requests are routed by a globally distributed load-balancer to the nearest geo-localised zone; it is currently deployed across 3 main regions: Asia (northeast), Europe (west) and USA (east). In each geo-localised region, the infrastruture decribed below is mantained
  • An auto-scalable group of API instances which interprets GraphQL queries and serves the required data from,
  • another auto-scalable group of high-performance ClickHouse DB instances, through
  • an internal TCP regional load-balancer which makes transparent and high-available the number of ClickHouse nodes running at any period of time.
The API, which also acts as a playground where you can interactively execute GraphQL queries and play with real data, is written in Scala with Play framework using Sangria as a server-side GraphQL implementation.
The front-end is written using the React javascript library and is hosted on Netlify.
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