"BaseSpace Apps- Is One Enough?' Biomatters' CTO D.Matt Landry on Bioinformatics 3.0


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Biomatters' CTO D.Matt Landry gave a presentation titled 'BaseSpace Apps- Is One Enough?' at Illumina's BaseSpace Worldwide Developer meeting.

#basedev2013, #bioinformatics 3.0

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"BaseSpace Apps- Is One Enough?' Biomatters' CTO D.Matt Landry on Bioinformatics 3.0

  1. 1. BaseSpace Apps IS ONE ENOUGH? D Matthew Landry, CTO dmlandry@biomatters.com dmlandry ! ILMN BaseSpace Worldwide Developer’s Mtg, 21 Oct 2013 This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License
  2. 2. Disclosure I have no actual or potential conflict of interest in relation to this presentation. Except the obvious:
  3. 3. Bioinformatics 1.0 ⟶ 3.0 Technology like BaseSpace We almost got it wrong
  4. 4. Bioinformatics 1.0
  5. 5. #!/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
  6. 6. Bioinformatics 2.0
  7. 7. 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 ...
  8. 8. Bioinformatics 3.0
  9. 9. Bioinformatics 3.0 ClinVar
  10. 10. How does this change
 the way we build apps?
  11. 11. 12 20 10 20 08 20 06 20 04 20 02 20
  12. 12. Recreate Geneious CSS/Javascriptery Monolithic web app
  13. 13. No desktop limits Data quanta increasing Structured pipelines
  14. 14. Foundation platform Apply best-in-class tools Channel to users
  15. 15. FLT3 KIT CEBPA SPI1 JUP CCNA1 PIM1 CCND1 TCF7 TCF7L2 TCF7L1 t14 t197 t56 t254 t299 t76 t256 t150 AKT3 AKT1 t88 AKT2 SOS2 t22 t144 t169 SOS1 t303 t237 t190 t127 t99 t87 t35 t147 t258 t217 t66 t158 t200 t171 t298 t286 t179 t98 t284 t208 t90 t89 t278 t175 t143 t39 t34 t255 t38 t155 t163 t125 t86 t31 t17 t226 t108 t85 t82 t78 t70 t60 t132 t213 t308 t172 t148 t37 t119 t29 t212 t94 t77 t106 t269 t272 t28 t202 t149 t206 t92 t141 t156 t218 t170 t101 t59 t283 t219 t32 t44 t81 t161 t134 t80 t64 t136 t46 t128 t215 t146 t100 t21 t43 t309 t307 t305 t302 t297 MTOR CHUK BAD IKBKB IKBKG HRAS t296 t295 t294 KRAS NRAS t287 t281 t279 t275 t268 t267 t266 t253 t244 t239 t236 t233 t231 t229 t228 t222 t204 t203 t198 t194 t193 t189 t186 t178 t176 t174 t168 t167 t166 t164 t162 t157 t154 t151 t142 t139 t138 t131 t129 t126 t124 t117 t115 t113 t110 t109 t104 t102 t93 t84 t83 t79 t75 t74 t73 t71 t69 t67 t65 t63 t50 t47 t42 t36 t27 t23 t20 t18 t16 t180 t145 t246 t183 t26 t160 t62 t310 t207 t182 t235 t173 t260 t241 t15 t140 t30 t184 t221 t188 RPS6KB2 EIF4EBP1 RPS6KB1 NFKB1 RELA PIK3CG t247 t33 t12 PIK3CB PIK3R1 RAF1 BRAF ARAF This.Tumor t261 t199 t248 t216 t68 t227 t293 t300 t285 t264 t263 t262 t259 t245 t243 t242 t240 t238 t225 t214 t211 t201 t196 t195 t159 t130 t123 t122 t91 t72 t58 t53 t24 t19 t11 t289 t152 t291 t265 t111 t282 t187 t177 t223 t165 t45 t95 t40 t306 t153 t273 t249 t181 t277 t25 t107 t292 t290 t135 t103 t10 t232 t210 t41 t118 t220 t9 t133 t1 t120 t205 t48 t304 t301 t288 t280 t276 t274 t271 t270 t257 t252 t251 t250 t234 t230 t224 t209 t192 t191 t185 MAP2K1 MAP2K2 MAPK1 MAPK3 t137 t121 t116 t114 t112 t105 t97 t96 t61 t57 t55 t54 t52 t51 t49 t13 t8 t7 t6 t5 t4 t3 BAD KRAS IKBKG CEBPA PIK3R3 EIF4EBP1 TCF7 AKT3 RPS6KB2 CHUK PIK3CD RPS6KB1 PML AKT1 ARAF HRAS MYC PIK3R2 PIM2 RARA PPARD MAPK3 SPI1 IKBKB LEF1 RAF1 STAT5B AKT2 RELA GRB2 TCF7L2 SOS2 PIK3R1 STAT3 CCND1 TCF7L1 MAP2K2 RUNX1 MAPK1 STAT5A KIT JUP PIM1 CCNA1 PIK3R5 PIK3CA PIK3CB MAP2K1 FLT3 SOS1 MTOR NFKB1 ZBTB16 BRAF NRAS PIK3CG t2 RUNX1T1 PML LEF1 AKT1 RARA CHUK STAT3 MAPK3 RAF1 PPARD PIK3R5 RELA IKBKB TCF7L2 ZBTB16 KIT FLT3 HRAS STAT5B PIM1 GRB2 CCND1 JUP MYC PIM2 PIK3R2 PIK3R1 MTOR RUNX1 MAP2K2 RPS6KB1 AKT2 SOS2 MAPK1 STAT5A PIK3CG SPI1 SOS1 CCNA1 PIK3CA MAP2K1 TCF7 PIK3CB TCF7L1 RUNX1T1 AKT3 BRAF NRAS NFKB1 PIK3CD BAD ARAF KRAS IKBKG CEBPA PIK3R3 RPS6KB2 STAT5B Melanomagenesis.Drivers..Flahertyet.al. t18 t16 t20 t23 t27 t36 t42 t47 t50 t63 t65 t67 t69 t71 t73 t74 t75 t79 t83 t84 t93 t102 t104 t109 t110 t113 t115 t117 t124 t126 t129 t131 t138 t139 t142 t151 t154 t157 t162 t164 t166 t167 t168 t174 t176 t178 t186 t189 t193 t194 t198 t203 t204 t222 t228 t229 t231 t233 t236 t239 t244 t253 t266 t267 t268 t275 t279 t281 t287 t294 t295 t296 t297 t302 t305 t307 t309 t148 t37 t172 t308 t241 t15 t56 t299 t76 t132 t181 t213 t254 t283 t44 t81 t9 t19 t11 t24 t53 t58 t72 t91 t122 t123 t130 t159 t195 t196 t201 t211 t214 t225 t238 t240 t242 t243 t245 t259 t262 t263 t264 t285 t300 t33 t12 t70 t60 t78 t82 t85 t108 t226 t17 t21 t202 t149 t28 t158 t286 t179 t298 t171 t217 t155 t38 t219 t32 t39 t94 t77 t212 t29 t98 t175 t143 t278 t90 t89 t255 t272 t269 t197 t145 t246 t30 t183 t26 t87 t35 t99 t127 t190 t237 t303 t86 t31 t125 t150 t144 t163 t169 t22 t34 t119 t43 t46 t101 t59 t170 t218 t62 t66 t68 t134 t80 t161 t88 t206 t92 t100 t106 t128 t136 t140 t141 t156 t64 t146 t235 t173 t160 t177 t184 t188 t187 t221 t199 t200 t208 t182 t210 t215 t120 t216 t227 t247 t290 t135 t273 t249 t153 t260 t284 t289 t292 t293 t306 t118 t265 t258 t180 t207 t14 t256 t147 t261 t1 t107 t25 t41 t95 t103 t111 t133 t223 t165 t220 t248 t282 t310 This.Tumor t277 t152 t291 t10 t45 t232 t40 t3 t2 t4 t5 t6 t7 t8 t13 t49 t51 t52 t54 t55 t57 t61 t96 t97 t105 t112 t114 t116 t121 t137 t185 t191 t192 t209 t224 t230 t234 t250 t251 t252 t257 t270 t271 t274 t276 t280 t288 t301 t304 t48 t205 EIF4EBP1 STAT5A Expression.associated.with.survival..Bogonovic.et.al. Melanomagenesis.Drivers..Flahertyet.al. STAT3 ZBTB16 Druggability..Sophic.Integrated Expression.associated.with.survival..Bogonovic.et.al. PML ClinicalTrials.gov.melanoma Druggability..Sophic.Integrated RARA DrugBank.drug.target ClinicalTrials.gov.melanoma RUNX1 PIM2 GRB2 DrugBank.drug.target RUNX1T1 PIK3R5 PIK3CA PIK3R3 PIK3R2 PIK3CD MYC LEF1 PPARD
  16. 16. Targeted Computational Dx 
 for applied laboratory genomics
  17. 17. Is one App enough?
  18. 18. One is not enough.
  19. 19. fin. dmlandry@biomatters.com dmlandry