WormBase database migration to Datomic on AWS: A case Study
summary
WormBase migrates its legacy ACeDB graph into Datomic on AWS, converting ACeDB → XML → EDN and importing events in historical order so the database contains 30 years of timestamped history. A custom REST API serves endpoints one at a time while the site drops heavy caching, cutting merge pain. Deployment uses Docker + Elastic Beanstalk, CloudFormation to spawn a transactor per release and DynamoDB per transactor; a small team iterates ongoing fixes and aims to finish within months.
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chapters (24)
- 0:00Introduction
- 1:00Who is Adam
- 1:50What does WormBase do
- 2:54Alan Turing quote
- 3:22Alan Turing in Biology
- 4:25Biology 101
- 5:51Model organisms
- 7:19What is WormBase
- 7:34Fullgrown Worm
- 7:59How it works
- 8:54WormBase website
- 9:34WormBase database
- 10:44Problems with AceDB
- 11:49Database selection
- 12:05Other databases
- 13:05Datomic
- 13:17Thomastown
- 14:24Takehome message
- 15:34Pipeline
- 18:16Diagram
- 20:02Architecture
- 21:53Future plans
- 28:12Cloud Formation
- 29:38Team
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