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

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

Nov 02, 2022 182 likes •493 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

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ONE CODEX

From biobanks to databanks?

Exploring the PathoMAP project

  • n the One Codex data platform

ONE CODEX

Nick Greenfield, Founder & CEO MetaSUB Summit, Shanghai, July 1st 2016

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ONE CODEX

Brief background (really!)

  • San Francisco-based

software company

  • Data platform offering

“sequence to answer” solution for microbial and metagenomics

  • Design goals include:

scalability, reproducibility, and ease-of-use

One Codex metagenomic analysis view

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ONE CODEX

  • San Francisco-based

software company

  • Data platform offering

“sequence to answer” solution for microbial and metagenomics

  • Design goals include:

scalability, reproducibility, and ease-of-use

Brief background (really!)

One Codex metagenomic analysis view

Data platform

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ONE CODEX

Biobanks...

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ONE CODEX

Advantages: Biological & “close to truth”; “multi-media”; vast historical archives

Biobanks...

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ONE CODEX

Disadvantages: Fragile, finite/depletable, expensive to use and maintain

Biobanks...

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ONE CODEX

... 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

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ONE CODEX

Complement biobanks: (Relatively) durable, distributable, (nearly) free analysis & re-analysis

... 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

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ONE CODEX

... 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

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ONE CODEX

... 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

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ONE CODEX

... 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

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ONE CODEX

... 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

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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ONE CODEX

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