Genomes On Rails
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Genomes On Rails

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Originally given at RailsConf, this talk outlines how the Wellcome Trust Sanger Institute is using Ruby and Rails as part of their new sequencing platform.

Originally given at RailsConf, this talk outlines how the Wellcome Trust Sanger Institute is using Ruby and Rails as part of their new sequencing platform.

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Genomes On Rails Genomes On Rails Presentation Transcript

  • Genomes on Rails has_many :sequences
  • Hello
  • ➊ Previously ➋ Production ➌ Process
  • ➊ Previously
  • The human genome 15 years to decode 3 billion letters
  • $3 billion
  • $3 billion ++
  • Race for the prize
  • Open data
  • Open source
  • Perl
  • Lots of Perl
  • Lots of Perl ~4500 modules
  • Onwards!
  • 40 species
  • Map evolutionary space
  • Compare genomes
  • compare species Compare genomes
  • compare species Compare genomes compa re indi viduals
  • More Perl ~1500 modules
  • Quantum leap!
  • 1000 personal genomes
  • beyond 23andme 1000 personal genomes
  • Hypertension
  • Diabetes
  • Coronary heart disease
  • Bipolar disorder
  • Malaria
  • ➋ Production
  • Register projects Register samples Sample prep Sequencing Analysis
  • Change!
  • Flexible data capture
  • Virtual fields
  • Sample Name Organism Concentration
  • class Sample < ActiveRecord::Base has_many :descriptors has_many :descriptor_values end
  • Key value pairs
  • Faster than you’d think
  • Change!
  • V1 V2 Sample Sample Name Name Organism Organism Concentration Concentration Origin Quality metric
  • Rationalize!
  • V1 V2 Sample Sample Name Name Organism Organism Concentration Concentration Origin Quality metric
  • Mapping!
  • V1 V3 Sample Sample Name Name Organism Species Concentration Concentration Origin Origin Quality metric
  • Pipeline management
  • Workflow Task 1 Task 2 Task 3 Name Name Name Operator Serial number Passed Instrument Kit
  • Throughput!
  • 320Tb 450 CPU
  • 320Tb 450 CPU Archive
  • 75 Tb
  • pilot study!
  • Multiple apps
  • Multiple instances
  • Loosely coupled
  • Loose coupling is hard
  • Deployment
  • Maintenance
  • Monitoring
  • Hard to maintain separation
  • Support novel science
  • Single code base
  • nginx reverse proxy
  • fairnginx
  • Mongrel
  • Fast deployment
  • Automate everything
  • Play well with others! Interoperability!
  • Legacy databases
  • RESTful services
  • Generate API stubs
  • SCALE!
  • Trillionics
  • 2 X
  • 150Tb per week
  • Over 6 months
  • More hardware
  • 400 additional nodes
  • additional 360 Tb
  • Towards a Virtual Institute
  • Lots of data
  • Lots of data, lots of people
  • Lots of data, lots of people, lots of compute
  • Lots of data, lots of people, lots of compute, lots of uses
  • Lots of data, lots of people, lots of compute, lots of uses, lots and lots and lots and lots...
  • ➌ Process
  • Concept Requirements Development Product
  • takes too lon g Concept Requirements Development Product
  • takes too lon g Concept Requirements Development Product the se change
  • Plan Development REVIEW Concept What we need Get ready
  • Focused
  • Project owner is key
  • Weekly releases
  • More flexible
  • Less time
  • Better transparency
  • Less software
  • Sequencing informatics
  • Thank you
  • GREENISGOOD.CO.UK