Serverless Beacon: Helping take genomic analysis from the cloud to - PowerPoint PPT Presentation

Serverless Beacon: Helping take genomic analysis from the cloud to the clinic Brendan Hosking October 2019, HISA Data Analytics 2019 HEALTH AND BIOSECURITY

Genomic data discovery: Beacons 2 | Custom Continuous Deployment to Uncover the Secrets in the Genome | Brendan Hosking Serverless Beacon: Helping take genomic analysis from the cloud to the clinic | Brendan Hosking

3 | Custom Continuous Deployment to Uncover the Secrets in the Genome | Brendan Hosking Serverless Beacon: Helping take genomic analysis from the cloud to the clinic | Brendan Hosking

Serverless-Beacon to scale up discovery across continents Powerful Cheaper “ Only pay for the “Scaling up to large resources volumes of consumed – zero distributed variant downtime cost. “ data.“ Used by 4 | Custom Continuous Deployment to Uncover the Secrets in the Genome | Brendan Hosking Serverless Beacon: Helping take genomic analysis from the cloud to the clinic | Brendan Hosking

Scaling Analysis Samples #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103 HG00105 HG00106 HG0 1 15820 rs2691315 G T 100 PASS AC=6;AN=20;VT=SNP;EX_TARGET GT 1|0 0|1 0|1 0|0 0|0 1| 1 15903 rs557514207 G GC 100 PASS AC=8;AN=20;VT=INDEL;EX_TARGET GT 0|1 0|1 0|0 1|0 0|1 0|0 1 69761 rs200505207 A T 100 PASS AC=2;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 0|0 0|0 1|1 0|0 Records 1 889159 rs13302945 A C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1 894573 rs13303010 G A 100 PASS AC=18;AN=20;VT=SNP;EX_TARGET GT 1|0 1|1 1|1 1|1 1|1 1|1 1 897216 rs186126206 C T 100 PASS AC=1;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 0|0 0|0 1|0 0|0 1 897325 rs4970441 G C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1 899928 rs6677386 G C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1 1564952 rs535125876;rs112177324 TG TGG,T 100 PASS AC=0,8;AN=20;VT=INDEL;MULTI_ALLELIC;EX_TARGET GT 2|2 0|0 0|0 Dataset Variant Call File Beacon #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103 HG00105 HG00106 HG00107 1 15820 rs2691315 G T 100 PASS AC=6;AN=20;VT=SNP;EX_TARGET GT 1|0 0|1 0|1 0|0 0|0 1|0 1|0 0|0 0|0 0|1 1 15903 rs557514207 G GC 100 PASS AC=8;AN=20;VT=INDEL;EX_TARGET GT 0|1 0|1 0|0 1|0 0|1 0|0 0|1 0|1 0|1 0|1 1 69761 rs200505207 A T 100 PASS AC=2;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 1 69897 rs200676709 T C 100 PASS AC=17;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 0|0 1|1 1|1 1|0 1|1 1|1 1|1 1|1 1 876499 rs4372192 A G 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 877831 rs6672356 T C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 878314 rs142558220 G C 100 PASS AC=2;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1 881070 rs41285794 G A 100 PASS AC=1;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 1 881627 rs2272757 G A 100 PASS AC=13;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 1|1 1|1 1|0 1|1 1|1 1|0 1|0 1|1 1 881918 rs35471880 G A 100 PASS AC=2;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 1 887560 rs3748595 A C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 887801 rs3828047 A G 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 888639 rs3748596 T C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 888659 rs3748597 T C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 889158 rs13303056 G C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 889159 rs13302945 A C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 894573 rs13303010 G A 100 PASS AC=18;AN=20;VT=SNP;EX_TARGET GT 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1 897216 rs186126206 C T 100 PASS AC=1;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 1 897325 rs4970441 G C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 899928 rs6677386 G C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 1564952 rs535125876;rs112177324 TG TGG,T 100 PASS AC=0,8;AN=20;VT=INDEL;MULTI_ALLELIC;EX_TARGET GT 2|2 0|0 0|0 2|0 0|2 2|0 0|2 2|0 2|0 1 878314 rs142558220 G C 100 PASS AC=2;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 1|1 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1 881070 rs41285794 G A 100 PASS AC=1;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 0|0 1 881627 rs2272757 G A 100 PASS AC=13;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 1|1 1|1 1|0 1|1 1|1 1|0 1|0 1|1 1 881918 rs35471880 G A 100 PASS AC=2;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 1|1 1 887560 rs3748595 A C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 887801 rs3828047 A G 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 888639 rs3748596 T C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 888659 rs3748597 T C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 889158 rs13303056 G C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 889159 rs13302945 A C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 894573 rs13303010 G A 100 PASS AC=18;AN=20;VT=SNP;EX_TARGET GT 1|0 1|1 1|1 1|1 1|1 1|1 1|1 1|0 1|1 1|1 1 897216 rs186126206 C T 100 PASS AC=1;AN=20;VT=SNP;EX_TARGET GT 0|0 0|0 0|0 0|0 1|0 0|0 0|0 0|0 0|0 0|0 1 897325 rs4970441 G C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 899928 rs6677386 G C 100 PASS AC=20;AN=20;VT=SNP;EX_TARGET GT 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1 1564952 rs535125876;rs112177324 TG TGG,T 100 PASS AC=0,8;AN=20;VT=INDEL;MULTI_ALLELIC;EX_TARGET GT 2|2 0|0 0|0 2|0 0|2 2|0 0|2 2|0 2| 0|0 5 | Serverless Innovation for Health | Denis C. Bauer | @allPowerde Serverless Beacon: Helping take genomic analysis from the cloud to the clinic | Brendan Hosking

Why Serverless? Expensive manual termination Cheapest Limited Must Provision size Scalable Insecure security policies Secure 6 | Serverless Innovation for Health | Denis C. Bauer | @allPowerde Serverless Beacon: Helping take genomic analysis from the cloud to the clinic | Brendan Hosking

Challenges Limits DevOps Memory No direct access Life span Slow Testing Loop Storage Function versions 7 | Serverless Innovation for Health | Denis C. Bauer | @allPowerde Serverless Beacon: Helping take genomic analysis from the cloud to the clinic | Brendan Hosking