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Talk from the Bioinformatics session of the Advances in Genome Biology and Technology 2009 meeting.
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Framing the problem
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Analysis - cDNASolexa cDNA reads
SNPsIndels
Gene expression
(to exquisite sensitivity)
[Transcriptome] OR [Genome + SpliceJunctions (SJs)] OR [Genome]
Variant discovery/
ASE
Splice isotypes
NovelGenes
Readdepth
Maq/Tophat
MaqReadsmap to
“non-genic”regions
VelvetGenScan
Readsmap to
novel SJs or introns
Changing pipelines - LIMSPrep
Tech-SpecificPrep /Detection
Primary Analysis
PCR
cDNAs
3730 Phred
Submission
HybridSelection
Bisulfite
SamplePooling
JumpingLibraries
WGS
Solexa
454
SOLiD
ChurchPolony(?)
Helicos(?)
…
(Technology-specific)
Flow-space
Color-space
.
.
.
NCBI Trace
ProjectArchives(e.g., DCC)
NCBI SRA
NCBI MedicalArchive
Courtesy of Toby Bloom
Changing pipelines - AnalysisBLASTBLATPASHssaha
runMappingELAND
mapreadsArachne
MAQexonerateSHRiMPSPLIGNMosaik
SLIM SearchSXOligoSearch
SOAP2NovoCraft
BowtieTophat
PhrapArachnePCAP
PhusionEuler
ATLASNewblerVelvetForge
SSAKEVCAKE
Euler-USRSHARCGS
CABOG
Alig
ners
Assem
blers
UR• Object-relational mapping (ORM) layer
– Interact with persistence layer (e.g., relational database) through objects and methods
– Automatic, dynamic class definitions– Moose1-like object definition syntax
• Object context– In-memory transactions (even across databases)– Caching/deferred loading
• Dynamic command-line interface• Integrated documentation system
1 - http://www.iinteractive.com/moose/
… but with a wrinkle• Lab personnel accept
the software you give them
• Analysts are more than happy to develop their own
• We need to make it easy for analysts to build tools within the system
Challenges• There is still much more work to do• Sequencing is demolishing Moore’s law• The cult of traces• The richness of data• Visualization
ThanksWeb Site http://genome.wustl.edu/Blog http://www.politigenomics.com/
LIMS Paper http://www.biomedcentral.com/1471-2105/8/362UR Presentation http://www.media-landscape.com/yapc/2006-06-27.ScottSmith/
