ISMB2008_Dawei_Lin_LIMS - Bioinformatics Core Wiki

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2 Οκτ 2013 (πριν από 4 χρόνια και 11 μέρες)

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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

800GB

200GB

Hundred of

thousands files

http://bioinformatics.ucdavis.edu

17 hours of copying

to a USB drive

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

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

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