Sequencescape - a cloud enabled laboratory information management system (LIMS) for second and third generation sequencing

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

3. Faculty view
DNA pipelines

4. • Support every technology on the block
• Primary pipelines are Solexa sequencing
and Genotyping
• Working at a different scale then most
people

5. Sample
management /
Reporting
LIMS
Run tracking/ Data
QC
Data archiving
Data analysis
Data
release

6. Faculty IT view

7. Key parts of LIMS
• Freezer tracking • Automation
• Aliquot tracking • Data release
• Information capture • Reporting
• Study management • Reagent tracking
• Capacity • Liquid handling
management • Workflows
• Back office

8. Organization of information
created from
contains
released as
based on
created from
child
parent
payed for by
processed in

9. Creating new lab pipelines

10. Development
• Incremental release every two weeks.
Larger projects run in more classical way.
• Developed directly on github

11. Show stoppers for sharing
• Local dependencies
• Differences in protocols
• Not wanting to share what is being done
• Trying to externalise them were possible

12. Example: Creating a new
pipeline

13. Alternatives
• Thermo Fisher – Nautilus
• Genologics
• WikiLIMS
• Excel or Google docs
• Sequencing companies/centers (still
needs tracking)

14. 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