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