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From biobanks to databanks? Exploring the PathoMAP project ONE - PowerPoint PPT Presentation

Nov 02, 2022 •182 likes •489 views

From biobanks to databanks? Exploring the PathoMAP project ONE CODEX on the One Codex data platform Nick Greenfield, Founder & CEO MetaSUB Summit, Shanghai, July 1 st 2016 ONE CODEX Brief background (really!) San Francisco-based

  1. From biobanks to databanks? Exploring the PathoMAP project ONE CODEX on the One Codex data platform Nick Greenfield, Founder & CEO MetaSUB Summit, Shanghai, July 1 st 2016 ONE CODEX

  2. Brief background (really!) • San Francisco-based software company • Data platform offering “sequence to answer” solution for microbial and metagenomics • Design goals include: scalability, reproducibility, One Codex metagenomic analysis view and ease-of-use ONE CODEX

  3. Brief background (really!) • San Francisco-based software company Data platform • Data platform offering “sequence to answer” solution for microbial and metagenomics • Design goals include: scalability, reproducibility, One Codex metagenomic analysis view and ease-of-use ONE CODEX

  4. Biobanks... ONE CODEX

  5. Biobanks... Advantages: Biological & “close to truth”; “multi-media”; vast historical archives ONE CODEX

  6. Biobanks... Disadvantages: Fragile, finite/depletable, expensive to use and maintain ONE CODEX

  7. ... to databanks? @HWI-D00151:75:H9AQQADXX:2:1101:11980:2239 2:N:0:GGACTCCTTATCCTCT AATTCAACGATACGCCAGCCCTTCGACAAACGGCTGTACCGATCTACCGCTTTACGTGGCCCGAGGCCATTGCCGCACCAGAGAGATGCGCTTAAGGTAC + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFBFFFFFFBBBBFFFFBBF<BFFFFFFBBBFFFFFFFFFFF @HWI-D00151:75:H9AW7ADXX:2:1101:14056:2237 2:N:0:GGACTCCTTATCCTCT GTATTGTAGAGCTGTCGATTAGCGTGTCGNTGATGGCCAAATGAAGGGCGACCGCGTCTGGCGTCGACGCTGACGCGTAACGCTTCGTGGTGCTGCAATT + BBBFFFFFFFFFFIFIIIIIIFFFII#0BBFFIIIIIIIIIIIIIIIIBFFFFFFFFFFFBFBFF<BBBFFFFFBFFFFFFFFFFFFBBF<BBFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:18423:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACAATGTATCCGCGGTCGCCGTAGTTGAAGGATGTGACGATAAACAGCATCACCACTATTTTCTCTTATACACATCTGACGCTGCGACGAAG + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1667:2337 2:N:0:GGACTCCTTATCCTCT CGCTATTAGTTGCCTGATTGAGCGTCTTCCGCCATGCGGGCATTGCTGCCTGGAGTGGCAACAGTGTCCGGAACAGGAACTGAATCGGCTAGGGAATGCA + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFFIIIIFFFFFBFFFFFFFFF<BBFBFBFFFBFFFFFFFFFFFFFBBBFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1848:2341 2:N:0:GGACTCCTTATCCTCT CAGAGCCGAAGACAAAAAGATGTCTGCAATAATGTAATGTACATATAGATCGATTGCGAGCATCATCGCAACTATGTGCTCATGGATTCTTCAACGTAAT + BBBFFFFFFFFFFIFFFFFBFFFIIIIIIIIIIIIIIFIIFIIIBFFFIIIIIFIIBFBFBFFFFFFFFFBBBBBB<BBBFFFBBBBBFFFFFBBBBFFF @HWI-D00151:75:H9AQQADXX:2:1101:1849:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACGTCAAATGTGGCGCGCCGTAGTTGAAGGATGTACGATAAAACAGCATCACCACTATTTGTCTCACGTTACACTCTGACGCTGCCGACGAA + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF ONE CODEX

  8. ... to databanks? @HWI-D00151:75:H9AQQADXX:2:1101:11980:2239 2:N:0:GGACTCCTTATCCTCT AATTCAACGATACGCCAGCCCTTCGACAAACGGCTGTACCGATCTACCGCTTTACGTGGCCCGAGGCCATTGCCGCACCAGAGAGATGCGCTTAAGGTAC + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFBFFFFFFBBBBFFFFBBF<BFFFFFFBBBFFFFFFFFFFF @HWI-D00151:75:H9AW7ADXX:2:1101:14056:2237 2:N:0:GGACTCCTTATCCTCT GTATTGTAGAGCTGTCGATTAGCGTGTCGNTGATGGCCAAATGAAGGGCGACCGCGTCTGGCGTCGACGCTGACGCGTAACGCTTCGTGGTGCTGCAATT + BBBFFFFFFFFFFIFIIIIIIFFFII#0BBFFIIIIIIIIIIIIIIIIBFFFFFFFFFFFBFBFF<BBBFFFFFBFFFFFFFFFFFFBBF<BBFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:18423:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACAATGTATCCGCGGTCGCCGTAGTTGAAGGATGTGACGATAAACAGCATCACCACTATTTTCTCTTATACACATCTGACGCTGCGACGAAG + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1667:2337 2:N:0:GGACTCCTTATCCTCT CGCTATTAGTTGCCTGATTGAGCGTCTTCCGCCATGCGGGCATTGCTGCCTGGAGTGGCAACAGTGTCCGGAACAGGAACTGAATCGGCTAGGGAATGCA + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFFIIIIFFFFFBFFFFFFFFF<BBFBFBFFFBFFFFFFFFFFFFFBBBFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1848:2341 2:N:0:GGACTCCTTATCCTCT CAGAGCCGAAGACAAAAAGATGTCTGCAATAATGTAATGTACATATAGATCGATTGCGAGCATCATCGCAACTATGTGCTCATGGATTCTTCAACGTAAT + BBBFFFFFFFFFFIFFFFFBFFFIIIIIIIIIIIIIIFIIFIIIBFFFIIIIIFIIBFBFBFFFFFFFFFBBBBBB<BBBFFFBBBBBFFFFFBBBBFFF @HWI-D00151:75:H9AQQADXX:2:1101:1849:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACGTCAAATGTGGCGCGCCGTAGTTGAAGGATGTACGATAAAACAGCATCACCACTATTTGTCTCACGTTACACTCTGACGCTGCCGACGAA + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF Complement biobanks: (Relatively) durable, distributable, (nearly) free analysis & re-analysis ONE CODEX

  9. ... to databanks? @HWI-D00151:75:H9AQQADXX:2:1101:11980:2239 2:N:0:GGACTCCTTATCCTCT AATTCAACGATACGCCAGCCCTTCGACAAACGGCTGTACCGATCTACCGCTTTACGTGGCCCGAGGCCATTGCCGCACCAGAGAGATGCGCTTAAGGTAC + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFBFFFFFFBBBBFFFFBBF<BFFFFFFBBBFFFFFFFFFFF @HWI-D00151:75:H9AW7ADXX:2:1101:14056:2237 2:N:0:GGACTCCTTATCCTCT GTATTGTAGAGCTGTCGATTAGCGTGTCGNTGATGGCCAAATGAAGGGCGACCGCGTCTGGCGTCGACGCTGACGCGTAACGCTTCGTGGTGCTGCAATT + BBBFFFFFFFFFFIFIIIIIIFFFII#0BBFFIIIIIIIIIIIIIIIIBFFFFFFFFFFFBFBFF<BBBFFFFFBFFFFFFFFFFFFBBF<BBFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:18423:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACAATGTATCCGCGGTCGCCGTAGTTGAAGGATGTGACGATAAACAGCATCACCACTATTTTCTCTTATACACATCTGACGCTGCGACGAAG + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1667:2337 2:N:0:GGACTCCTTATCCTCT CGCTATTAGTTGCCTGATTGAGCGTCTTCCGCCATGCGGGCATTGCTGCCTGGAGTGGCAACAGTGTCCGGAACAGGAACTGAATCGGCTAGGGAATGCA + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFFIIIIFFFFFBFFFFFFFFF<BBFBFBFFFBFFFFFFFFFFFFFBBBFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1848:2341 2:N:0:GGACTCCTTATCCTCT CAGAGCCGAAGACAAAAAGATGTCTGCAATAATGTAATGTACATATAGATCGATTGCGAGCATCATCGCAACTATGTGCTCATGGATTCTTCAACGTAAT + BBBFFFFFFFFFFIFFFFFBFFFIIIIIIIIIIIIIIFIIFIIIBFFFIIIIIFIIBFBFBFFFFFFFFFBBBBBB<BBBFFFBBBBBFFFFFBBBBFFF @HWI-D00151:75:H9AQQADXX:2:1101:1849:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACGTCAAATGTGGCGCGCCGTAGTTGAAGGATGTACGATAAAACAGCATCACCACTATTTGTCTCACGTTACACTCTGACGCTGCCGACGAA + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF ONE CODEX

  10. ... to databanks? @HWI-D00151:75:H9AQQADXX:2:1101:11980:2239 2:N:0:GGACTCCTTATCCTCT AATTCAACGATACGCCAGCCCTTCGACAAACGGCTGTACCGATCTACCGCTTTACGTGGCCCGAGGCCATTGCCGCACCAGAGAGATGCGCTTAAGGTAC + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFBFFFFFFBBBBFFFFBBF<BFFFFFFBBBFFFFFFFFFFF @HWI-D00151:75:H9AW7ADXX:2:1101:14056:2237 2:N:0:GGACTCCTTATCCTCT GTATTGTAGAGCTGTCGATTAGCGTGTCGNTGATGGCCAAATGAAGGGCGACCGCGTCTGGCGTCGACGCTGACGCGTAACGCTTCGTGGTGCTGCAATT + BBBFFFFFFFFFFIFIIIIIIFFFII#0BBFFIIIIIIIIIIIIIIIIBFFFFFFFFFFFBFBFF<BBBFFFFFBFFFFFFFFFFFFBBF<BBFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:18423:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACAATGTATCCGCGGTCGCCGTAGTTGAAGGATGTGACGATAAACAGCATCACCACTATTTTCTCTTATACACATCTGACGCTGCGACGAAG + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1667:2337 2:N:0:GGACTCCTTATCCTCT CGCTATTAGTTGCCTGATTGAGCGTCTTCCGCCATGCGGGCATTGCTGCCTGGAGTGGCAACAGTGTCCGGAACAGGAACTGAATCGGCTAGGGAATGCA + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFFIIIIFFFFFBFFFFFFFFF<BBFBFBFFFBFFFFFFFFFFFFFBBBFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1848:2341 2:N:0:GGACTCCTTATCCTCT CAGAGCCGAAGACAAAAAGATGTCTGCAATAATGTAATGTACATATAGATCGATTGCGAGCATCATCGCAACTATGTGCTCATGGATTCTTCAACGTAAT + BBBFFFFFFFFFFIFFFFFBFFFIIIIIIIIIIIIIIFIIFIIIBFFFIIIIIFIIBFBFBFFFFFFFFFBBBBBB<BBBFFFBBBBBFFFFFBBBBFFF @HWI-D00151:75:H9AQQADXX:2:1101:1849:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACGTCAAATGTGGCGCGCCGTAGTTGAAGGATGTACGATAAAACAGCATCACCACTATTTGTCTCACGTTACACTCTGACGCTGCCGACGAA + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF Requirements: Security, scalability, ease-of-use ( and extensibility), and reproducibility ONE CODEX

  11. ... to databanks? @HWI-D00151:75:H9AQQADXX:2:1101:11980:2239 2:N:0:GGACTCCTTATCCTCT AATTCAACGATACGCCAGCCCTTCGACAAACGGCTGTACCGATCTACCGCTTTACGTGGCCCGAGGCCATTGCCGCACCAGAGAGATGCGCTTAAGGTAC + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFBFFFFFFBBBBFFFFBBF<BFFFFFFBBBFFFFFFFFFFF @HWI-D00151:75:H9AW7ADXX:2:1101:14056:2237 2:N:0:GGACTCCTTATCCTCT GTATTGTAGAGCTGTCGATTAGCGTGTCGNTGATGGCCAAATGAAGGGCGACCGCGTCTGGCGTCGACGCTGACGCGTAACGCTTCGTGGTGCTGCAATT + BBBFFFFFFFFFFIFIIIIIIFFFII#0BBFFIIIIIIIIIIIIIIIIBFFFFFFFFFFFBFBFF<BBBFFFFFBFFFFFFFFFFFFBBF<BBFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:18423:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACAATGTATCCGCGGTCGCCGTAGTTGAAGGATGTGACGATAAACAGCATCACCACTATTTTCTCTTATACACATCTGACGCTGCGACGAAG + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1667:2337 2:N:0:GGACTCCTTATCCTCT CGCTATTAGTTGCCTGATTGAGCGTCTTCCGCCATGCGGGCATTGCTGCCTGGAGTGGCAACAGTGTCCGGAACAGGAACTGAATCGGCTAGGGAATGCA + BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFIIIFFIIIIFFFFFBFFFFFFFFF<BBFBFBFFFBFFFFFFFFFFFFFBBBFFFFFF @HWI-D00151:75:H9AQQADXX:2:1101:1848:2341 2:N:0:GGACTCCTTATCCTCT CAGAGCCGAAGACAAAAAGATGTCTGCAATAATGTAATGTACATATAGATCGATTGCGAGCATCATCGCAACTATGTGCTCATGGATTCTTCAACGTAAT + BBBFFFFFFFFFFIFFFFFBFFFIIIIIIIIIIIIIIFIIFIIIBFFFIIIIIFIIBFBFBFFFFFFFFFBBBBBB<BBBFFFBBBBBFFFFFBBBBFFF @HWI-D00151:75:H9AQQADXX:2:1101:1849:2248 2:N:0:GGACTCCTTATCCTCT GGCAATGGACGTCAAATGTGGCGCGCCGTAGTTGAAGGATGTACGATAAAACAGCATCACCACTATTTGTCTCACGTTACACTCTGACGCTGCCGACGAA + BBBFFFFFFFFFFIIIIIIIIIFIIIIIFIIIIIIIIIIIIFIIIIFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFF ONE CODEX

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