Credit: Tara Brown Photography/University of Washington ... · Yazdi et al., Scientific Reports,...

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Transcript of Credit: Tara Brown Photography/University of Washington ... · Yazdi et al., Scientific Reports,...

Page 1: Credit: Tara Brown Photography/University of Washington ... · Yazdi et al., Scientific Reports, 2017; Organick et al., Nature Biotechnology, 2018; Lopez et al., Nature Communications,
Page 2: Credit: Tara Brown Photography/University of Washington ... · Yazdi et al., Scientific Reports, 2017; Organick et al., Nature Biotechnology, 2018; Lopez et al., Nature Communications,

Credit: Tara Brown Photography/University of Washington Credit: Philipp Stössel/ETH Zurich Credit: Illumina

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Bases:

Data: Bits Base

00 A

01 C

10 G

11 T

Simple mapping:

Store data in synthetic DNA strands

…

150 to 300 bases

G T

TT G GG T G GT

10000111001001

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Ceze, Nivala and Strauss, Nature Reviews Genetics, 2019

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RandomAccessEncoding Synthesis Sequencing

(write)

1

0

0

0

1

0

1

0

1

1

G

C

A

C

T Preservation

G T(read)

Decoding

Electronic ElectronicMolecular 1

0

0

0

1

0

1

0

1

1

G

C

A

C

T

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First fully automated DNA data storage system

G T

synthesis

storage &

prep

sequencing

digital

microfluidics

Takahashi et al., Nature Scientific Reports, 2019

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Versatile platform to implement wet lab preparation protocols

VV

Newman et al., Nature Communications, 2019; Willsey, ASPLOS, 2019

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def thermocycle(droplet, temps_and_times):for temp, time in temps_and_times:

heat(droplet, temp, time)if droplet.volume < MIN_VOLUME:

droplet += input("water", min_volume)

def pcr(droplet, n_iter):thermocycle(droplet, n_iter * [

(95, 3 * minutes),(62, 30 * seconds),(72, 20 * seconds),

])

High-level

programming

with Puddle

Hardware

“Assembly code” activate(3,0)activate(3,1)activate(3,2)

…

Microfluidic Chips

Molecular

Computing

Synthetic DNA

Domain Specific Reasoning

Hardware Abstraction

Core Fluidic Semantics

ExperimentMedical

Diagnostics

Chemistry Medicine

Willsey et al., ASPLOS, 2019

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RandomAccessEncoding Synthesis Sequencing

(write)

1

0

0

0

1

0

1

0

1

1

G

C

A

C

T Preservation

G T(read)

Decoding

Electronic ElectronicMolecular 1

0

0

0

1

0

1

0

1

1

G

C

A

C

T

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AC GTCTCTGAACGT TGCA

AC CTCTCAGAACGT TGCA

AC CTCTGTGAACGT TGCA

AC GACTCTGAACGT TGCA

Force direction

1.8nm

Yazdi et al., Scientific Reports, 2017; Organick et al., Nature Biotechnology, 2018; Lopez et al., Nature Communications, 2019

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Force direction

1.8nm

Yazdi et al., Scientific Reports, 2017; Organick et al., Nature Biotechnology, 2018; Lopez et al., Nature Communications, 2019

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Problem: shifts complexity from time to amount of material

Hamiltonian path problemNode 1

G GT G

Node 2

TT GG G

Edge B

C AC C C

Adleman, DNA1, 1994

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Operate over data already stored in DNA

Target polynomial time algorithms

Extremely parallel and energy efficient10000111001000001 10101010

10000111001000001 11011101

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Double helix: complete match

Exploiting matches for exact and approximate search

T TT G GG TGGT

TG G T T GG

Good partial match Poor partial match

TG G

T T GG

TT

G GG TGGTT GT

G GGT

GG

T

T G

TG G

T TGG

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Good partial match

Poor partial match

Perfect match

CTACGG A T C TC A GCAGT3x

3x

3x

9x

TT G GG T G GT

TT A G GA C G C T G C AGATC

Magnetic

nanoparticle

CTACGG A T C TC A GCAGT

GT A C G CTAA CCT C AG AG

TAG GA T CT C C AGG GG A T

3x

2x

1x

GTA C

GCTAA CCT C AG AG

TT

AG GA C

GC T G C AGAT

C

TAG

GAT

CT CC A

GGGG A T

TTA

G GA CG

C TG

CA

GA

TC

Match-dependent yield

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image 2 ACGTAAGTCAGCGTGACTACGTAG

image 5 TCGATCTGAGTAAGTCGCGTAGTA

image 6 GTCAGGCGTACTTAGCTGATGACT

image 8 AGTCATGCGCGTACTCGTAGCTGA

Database/ training

Query/

inference CTGTGTAAGTCGTATAGTA

image 5

Stewart et al., DNA24, 2018

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image 2 ACGTAAGTCAGCGTGACTACGTAG

image 5 TCGATCTGAGTAAGTCGCGTAGTA

image 6 GTCAGGCGTACTTAGCTGATGACT

image 8 AGTCATGCGCGTACTCGTAGCTGA

Database/ training

Query/

inference CTGTGTAAGTCGTATAGTA

GACACATTCAGCATATCAT

image 5

Stewart et al., DNA24, 2018

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image 2

image 5 TCGATCTGAGTAAGTCGCGTAGTA

image 6

image 8

Database/ training

Query/

inference

GACACATTCAGCATATCAT

image 5

Stewart et al., DNA24, 2018

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ABSTRACT - textroad.com. Basic. Appl. Sci. Res., 3(1s... · Yazdi et al., 2013 nature to two sections of animate and inanimate, Ecotourism includes the study of animate nature and

ABSTRACT - textroad.com. Basic. Appl. Sci. Res., 3(1s... · Yazdi et al., 2013 nature to two sections of animate and inanimate, Ecotourism includes the study of animate nature and

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The Kasîdah (couplets) of Hâjî Abdû al-Yazdi [pseud.] a ... Kasidah/kasdahcouplets00bur… · PUBLISHER'SNOTE ThatTheKasidahofSirRichardFrancisBurtonwilleventually ranknextafterFitz-Gerald'sRuhdiydtisnotnecessarilyanuncriticalaffirmation

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