Sequencescape

Lars G. T. Jorgensen <lj3@sanger.ac.uk>

Faculty view

DNA pipelines

•  Support every technology on the block •  Primary pipelines are Solexa sequencing

and Genotyping •  Working at a different scale then most

people

Sample management /

Reporting

LIMS

Data archiving Data analysis

Data release

Run tracking/ Data QC

Faculty IT view

Key parts of LIMS

•  Freezer tracking •  Aliquot tracking •  Information capture •  Study management •  Capacity

management •  Back office

•  Automation •  Data release •  Reporting •  Reagent tracking •  Liquid handling •  Workflows

Organization of information

created from

based on

contains

parent child payed for by

released as

created from

processed in

Creating new lab pipelines

Development •  Incremental release every two weeks.

Larger projects run in more classical way. •  Developed directly on github

Show stoppers for sharing

•  Local dependencies •  Differences in protocols •  Not wanting to share what is being done •  Trying to externalise them were possible

Example: Creating a new pipeline

Alternatives

•  Thermo Fisher – Nautilus •  Genologics •  WikiLIMS •  Excel or Google docs •  Sequencing companies/centers (still

needs tracking)

Need your input •  What do you need from a LIMS? •  What information do you capture? •  What do you see the role of a LIMS

being?

http://www.sanger.ac.uk/resources/software/npg

http://github.com/sanger