1. Dawei Lin, Ph.D. Director, Bioinformatics Core UC Davis Genome Center http://bioinformatics.ucdavis.edu July 20, 2008, ISMB @ SLIMS (Solexa sequencing Laboratory Information Management System)

2. Next Gen Sequencing Applications Deep Sequencing (de novo, resequencing) SNP discovery ChIP-Seq SAGE Run-through Sequencing Digital Expression Profiling …… http://bioinformatics.ucdavis.edu

3. Illumina Sequencing Data 800GB 200GB Hundred of thousands files http://bioinformatics.ucdavis.edu 17 hours of copying to a USB drive

4. Core Facility Specific Issues Stable and reliable Infrastructure Privacy - Multiple Customers Data Sharing Web access Interoperability Recharge Each lane can belong to different customer http://bioinformatics.ucdavis.edu

5. Illumina Genome Analyzer (GA) 1TB/per data set per 3 days Solexa Server for image processing and base calling ( 2 Intel Xeon E5345 Quad-core 2.33GHz, 16GB RAM, ~8TB ) Processing time ~30 hours/data set Data retention time Up to 4 weeks (no long term storage) Copy on the fly Solexa Sequencing Data Flow (This infrastructure can hold two copies of data at least for three months) Linux Cluster alignment & assembly Sun Storagetek Tape Backup Library Online Data Access Server Sun Thumper x4500 (48TB) Data retention time up to 3 months 2 nd copy Web access Secure Shell access 1 st copy Mobile hard drive Data retention time – user specified 2 month Free access Mobile hard drive Self service recharge Disk to Disk backup/ Redundant Server http://bioinformatics.ucdavis.edu

6. SLIMS workflow GA operation MySQL Central Storage Access VM rsych Web

7. Future Directions Open Source (http://trac.genomecenter.ucdavis.edu)http://trac.genomecenter.ucdavis.edu OpenID Integrated with different pipelines BioCloud

8. Acknowledgement Adam Schaal DB Programmer Brad Sickler System Programmer Charlie Nicolet Director of DNA technology Core Dawei Lin (lhslin@ucdavis.edu, http://bioinformatics.ucdavis.edu)lhslin@ucdavis.edu

9. Run view

10. Lane view

11. Summary

12. View files folder

13. Create a run

14. Status of rsync between different servers

16. Documentation