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