"basespace apps- is one enough?' biomatters' cto d.matt landry on bioinformatics 3.0
TRANSCRIPT
BaseSpace Apps
IS ONE ENOUGH?
D Matthew Landry, CTO [email protected] dmlandry
!ILMN BaseSpace Worldwide Developer’s Mtg, 21 Oct 2013
This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License
I have no actual or potential conflict of interest in relation to this presentation.
Disclosure
Except the obvious:
Bioinformatics 1.0 ⟶ 3.0
Technology like BaseSpace
We almost got it wrong
Bioinformatics 1.0
#!/usr/bin/env bash /bin/BWA/bwa aln -f /output/FOO.sai -t 3 /seq/REFERENCE/human_18.fasta /seq/FQ/FOO.sanger.fq /bin/BWA/bwa samse -f /output/FOO.sam /seq/REFERENCE/human_18.fasta /output/FOO.sai /seq/FQ/FOO.sanger.fq /bin/SAMTOOLS/samtools import /seq/REFERENCE/human_18.fasta /output/FOO.sam /output/FOO.bam /bin/SAMTOOLS/samtools sort /output/FOO.bam /output/FOO.sorted /bin/SAMTOOLS/samtools index /output/FOO.sorted.bam /output/FOO.sorted.bam.bai java -jar /bin/GTK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /seq/REFERENCE/human_18.fasta -I /output/FOO.sorted.bam -o /output/FOO.intervals java -jar /bin/GTK/GenomeAnalysisTK.jar -T IndelRealigner -R /seq/REFERENCE/human_18.fasta -I /output/FOO.sorted.bam -targetIntervals /output/FOO.intervals --output /output/FOO.sorted.realigned.bam /bin/SAMTOOLS/samtools index /output/FOO.sorted.realigned.bam /output/FOO.sorted.realigned.bam.bai
Bioinformatics 2.0
Features - Genome browser - Annotation tracks - Genome assembly - Contig reporting - Read mapping - SNV detection - CNV detection - Differential expression - Microarray, RNA-seq - Epigenomics, ChIP-seq - NGS demultiplexing - DNA/RNA prediction - Primer design - In silico PCR - Molecular cloning - NCBI searching ...
Bioinformatics 3.0
Bioinformatics 3.0
ClinVar
How does this change the way we build apps?
2010
2002
2004
2006
2008
2012
Recreate Geneious
CSS/Javascriptery
Monolithic web app
No desktop limits
Data quanta increasing
Structured pipelines
Foundation platform
Apply best-in-class tools
Channel to users
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CHUK
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PIK3R5
MTOR
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ARAF
JUP
KIT
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PML
MAP2K1 MAP2K2
RAF1
RARA
SOS1SOS2
BRAF
STAT3 STAT5A STAT5B
ZBTB16
PIK3R3
IKBKG
RUNX1RUNX1T1
BAD
NFKB1 RELA
CEBPA SPI1
EIF4EBP1 RPS6KB1RPS6KB2
MYC LEF1 PPARDCCND1 TCF7 TCF7L2 TCF7L1
CCNA1
MAPK1 MAPK3
PIM2 PIM1
DrugBank.drug.target
ClinicalTrials.gov.melanoma
Druggability..Sophic.Integrated
Expression.associated.with.survival..Bogonovic.et.al.
Melanomagenesis.Drivers..Flahertyet.al.
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NRAS
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RAF
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MAP
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RAR
A
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PIK3R2
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HRAS
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CHUK
TCF7
RPS
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PIK3CD
AKT3
RPS
6KB2
PIK3R3
EIF4EB
P1
CEB
PA
BAD
IKBK
G
KRAS
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t167
t168
t174
t176
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t193
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t150
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t299
t254
t56
t197
t14
DrugBank.drug.target
ClinicalTrials.gov.melanoma
Druggability..Sophic.Integrated
Expression.associated.with.survival..Bogonovic.et.al.
Melanomagenesis.Drivers..Flahertyet.al.
RPS
6KB2
PIK3R3
EIF4EB
P1
CEB
PA
BAD
KRAS
IKBK
G
ARAF
AKT3
NFK
B1
BRAF
PIK3CD
NRAS
TCF7L1
TCF7
RUNX1T1
PIK3CB
SPI1
CCNA1
SOS1
MAP
2K1
PIK3CA
AKT2
STAT5A
PIK3CG
MAP
K1
SOS2
RPS
6KB1
MAP
2K2
MTO
R
RUNX1 JUP
PIM2
PIK3R1
MYC
PIK3R2
PIM1
CCND1
KIT
GRB2
FLT3
STAT5B
HRAS
RELA
ZBTB
16
RAF
1
IKBK
B
TCF7L2
PIK3R5
PPAR
D
MAP
K3
STAT3
RAR
A
PML
AKT1
CHUK
LEF1
t205t48t304t301t288t280t276t274t271t270t257t252t251t250t234t230t224t209t192t191t185t137t121t116t114t112t105t97t96t61t57t55t54t52t51t49t13t8t7t6t5t4t2t3t40t232t45t10t291t152t277This.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
Targeted Computational Dx for applied laboratory genomics
Is one App enough?
One is not enough.
