Post on 19-Dec-2015
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)
Next Gen Sequencing Applications
• Deep Sequencing (de novo, resequencing)• SNP discovery• ChIP-Seq• SAGE• Run-through Sequencing• Digital Expression Profiling• ……
http://bioinformatics.ucdavis.edu
Illumina Sequencing Data
QuickTime™ and a decompressor
are needed to see this picture.
800GB 200GB
Hundred of thousands files
http://bioinformatics.ucdavis.edu
17 hours of copyingto a USB drive
Core Facility Specific Issues
• Stable and reliable Infrastructure
• Privacy - Multiple Customers
• Data Sharing
• Web access
• Interoperability
• Recharge
QuickTime™ and a decompressor
are needed to see this picture. Each lanecan belongto differentcustomer
http://bioinformatics.ucdavis.edu
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 setData retention timeUp 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 ServerSun Thumper x4500 (48TB)Data retention time up to 3 months
2nd copy
Web access
Secure Shell access
1st copy
Mobile hard drive
Data retention time – user specified
2 monthFree access
Mobile hard drive
Self service
recharge
Disk to Disk backup/Redundant Server
http://bioinformatics.ucdavis.edu
SLIMS workflow
GA operation
MySQL Central Storage
Access VM
rsych
Web
Future Directions
• Open Source (http://trac.genomecenter.ucdavis.edu)
• OpenID
• Integrated with different pipelines
• BioCloud
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)
Run view
Lane view
Summary
View files folder
Create a run
Status of rsync between different servers
Status of rsync between different servers
Documentation