Download - Next-Generation Informatics
![Page 3: Next-Generation Informatics](https://reader033.vdocument.in/reader033/viewer/2022052321/5550444ab4c90580748b4cb1/html5/thumbnails/3.jpg)
Framing the problem
!"""# !""$# !""!# !""%# !""&# !""'# !""(# !"")# !""*# !""+# !"$"#
,--./01#234#
567#
89-.3:/#;<=>#
8/?@/AB/#
6/.1-AA/C#
![Page 9: Next-Generation Informatics](https://reader033.vdocument.in/reader033/viewer/2022052321/5550444ab4c90580748b4cb1/html5/thumbnails/9.jpg)
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
![Page 12: Next-Generation Informatics](https://reader033.vdocument.in/reader033/viewer/2022052321/5550444ab4c90580748b4cb1/html5/thumbnails/12.jpg)
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
![Page 13: Next-Generation Informatics](https://reader033.vdocument.in/reader033/viewer/2022052321/5550444ab4c90580748b4cb1/html5/thumbnails/13.jpg)
Changing pipelines - AnalysisBLASTBLATPASHssaha
runMappingELAND
mapreadsArachne
MAQexonerateSHRiMPSPLIGNMosaik
SLIM SearchSXOligoSearch
SOAP2NovoCraft
BowtieTophat
PhrapArachnePCAP
PhusionEuler
ATLASNewblerVelvetForge
SSAKEVCAKE
Euler-USRSHARCGS
CABOG
Alig
ners
Assem
blers
![Page 20: Next-Generation Informatics](https://reader033.vdocument.in/reader033/viewer/2022052321/5550444ab4c90580748b4cb1/html5/thumbnails/20.jpg)
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/
![Page 24: Next-Generation Informatics](https://reader033.vdocument.in/reader033/viewer/2022052321/5550444ab4c90580748b4cb1/html5/thumbnails/24.jpg)
… 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
![Page 31: Next-Generation Informatics](https://reader033.vdocument.in/reader033/viewer/2022052321/5550444ab4c90580748b4cb1/html5/thumbnails/31.jpg)
Challenges• There is still much more work to do• Sequencing is demolishing Moore’s law• The cult of traces• The richness of data• Visualization
![Page 33: Next-Generation Informatics](https://reader033.vdocument.in/reader033/viewer/2022052321/5550444ab4c90580748b4cb1/html5/thumbnails/33.jpg)
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/