Oligoarchive - Intelligent DNA Storage for Archival

Informazioni relative al progetto

OLIGOARCHIVE

ID dell’accordo di sovvenzione: 863320

DOI

10.3030/863320

Progetto chiuso

Data della firma CE 30 Agosto 2019

Data di avvio 1 Ottobre 2019

Data di completamento 31 Marzo 2023

Finanziato da

• EXCELLENT SCIENCE - Future and Emerging Technologies (FET)

Costo totale

€ 2 994 970,78

Contributo UE

€ 2 994 970,78

Coordinato da

IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE
United Kingdom

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Documents, reports (22)

Kick-off meeting

This deliverable entails the report including minutes of the kick-off meeting, agenda, list of participants.

Multiplexed PCR and sequencing for block addressing.

The methods which are part of this deliverable use multiplexed PCR to read out data from multiple oligos simultaneously

Analysis of Existing Protocols for Hybridisation

This deliverable entails a complete overview of tools and protocols for hybridisation needed for the join operation

Data cleaning techniques for database restoration.

This deliverable entails the methods which exploit the structured data to clean the data decoded

Integrated end-to-end prototype.

This deliverable entails the endtoend prototype from synthesis FRS or short oligos to storage to sequencing and decoding the result to binary format

Image storage pipeline for free-run synthesis.

The deliverable contains the methods and algorithms to encode imaging information in FRS longer 200 nucleotide oligos

Prototype of enzymatic DNA synthesis approach.

This deliverable entails a first prototype for enzymatic synthesis of long, FRS oligos.

Machine learning and clustering techniques for image restoration.

This deliverable entails the methods exploiting that machine learning models can be used to improve speed of decoding when some of the structure of the data is known

Methods to improve strand quality.

This deliverable entails new methods and protocols to improve stand quality of oligos resulting from enzymatic FRS

Official logo of OligoArchive, website and intranet portal.

The deliverable entails the web page (including social media if feasible), logo ant intranet portal of the project.

Prototype for scaleable DNA synthesis.

This deliverable entails methods to automate enzymatic FRS synthesis for very oligos

Structured database encoding techniques for short-strand synthesis.

The deliverable entails the methods needed to encode and decode structured databases into oligos Key is the exploitation of the inherent structure in databases to this end The result is algorithms documentation as well as experimental analysis

Adapting/redesigning encodings for free-run synthesis.

This deliverable entails the encodings and algorithms to do so for information storage in FRS oligos

Access-path-enabled functionality for imaging and databases.

Similarly this deliverable entails algorithms to implement access path for structure data and unstructured such as images

Encodings and protocols for the in-vitro join.

This deliverable entails the methods to encode the informationdatabase tuples such that they can be joined through hybridisation

Survey of Existing Encoding Techniques

This deliverable entails a survey of the state of the art in information encoding in DNA storage.

Access paths and data snapshoting based on block interface.

This deliverable contains the methods and algorithms to implement access paths for structure data based on a block interface

Image encoding techniques for short-strand synthesis.

This deliverable comprises the tools and techniques needed to encode images in short (<200 nucleotide) oligos. The deliverable includes algorithms as well as documentation for the algorithms.

Study of FRS and implication on encoding and protocols

This deliverable entails a study to understand how encodings need to be adapted for the error characteristics and biological constraints of FRS

Encodings/protocols for in-vitro selection and detection.

This deliverable entails protocols for content detection in oligos no matter the length encoding information

Completed communication activity.

See title

Database storage pipeline for free-run synthesis.

This deliverable entails the methods as a pipeline to encode structureddatabase data in long oligos

Pubblicazioni

Conference proceedings (17)

Nanopore Sequencing Simulator for DNA Data Storage

Autori: E. Gil San Antonio, T. Heinis, L. Carteron, M. Dimopoulou and M. Antonini
Pubblicato in: VCIP 2021, 2021
Editore: IEEE
DOI: 10.1109/vcip53242.2021.9675388

A constrained Shannon-Fano entropy coder for image storage in synthetic DNA

Autori: X. Pic, M. Antonini
Pubblicato in: EUSIPCO 2022, 2022
Editore: IEEE
DOI: 10.23919/eusipco55093.2022.9909833

DNA4DNA: Preserving Culturally Significant Digital Data with Synthetic DNA

Autori: Eugenio Marinelli, Eddy Ghabach, Thomas Bolbroe, Omer Sella, Thomas Heinis and Raja Appuswamy
Pubblicato in: iPRES 2021, 17th International Conference on Digital Preservation, 2021
Editore: N/A

Efficient Storage of Images onto DNA using Vector Quantization

Autori: Melpomeni Dimopoulou, Marc Antonini
Pubblicato in: 2020 Data Compression Conference (DCC), 2020, Pagina/e 363-363, ISBN 978-1-7281-6457-1
Editore: IEEE
DOI: 10.1109/dcc47342.2020.00085

Robust image coding on synthetic DNA: Reducing sequencing noise with inpainting

Autori: Eva Gil San Antonio; Mattia Piretti; Melpomeni Dimopoulou; Marc Antonini
Pubblicato in: https://hal.archives-ouvertes.fr/hal-03100971, Numero 2, 2020
Editore: IEEE
DOI: 10.1109/icpr48806.2021.9411920

Image storage in DNA using Vector Quantization

Autori: Melpomeni Dimopoulou, Marc Antonini
Pubblicato in: EUSIPCO, 2020
Editore: EURASIP

XJoin: Portable, parallel hash join across diverse XPU architectures with oneAPI

Autori: Marinelli, Eugenio; Appuswamy, Raja
Pubblicato in: DAMON, 2021
Editore: ACM

Digital Preservation with Synthetic DNA

Autori: Eugenio Marinelli, Eddy Ghabach, Thomas Bolbroe, Omer Sella, Thomas Heinis and Raja Appuswamy
Pubblicato in: BDA 2021, 37ème Conférence sur la Gestion de Données – Principles, Technologies et Applications, 2021
Editore: N/A

A JPEG-based image coding solution for data storage on DNA

Autori: Dimopoulou, Melpomeni; GIl, Eva; Antonini, Marc
Pubblicato in: EUSIPCO 2021, IEEE, 2021
Editore: IEEE

Optimizing the Accuracy of Randomized Embedding for Sequence Alignment

Autori: Yiqing Yan; Nimisha Chaturvedi; Raja Appuswamy
Pubblicato in: IPDPSW 2022, 2022
Editore: IEEE
DOI: 10.1109/ipdpsw55747.2022.00036

Generative DNA: Representation Learning for DNA-based Approximate Image Storage

Autori: Franzese, Giulio; Yan, Yiqing; Serra, Giuseppe; D’Onofrio, Ivan; Appuswamy, Raja; Michiardi, Pietro
Pubblicato in: VCIP 2021, 2021
Editore: IEEE
DOI: 10.1109/vcip53242.2021.9675366

Decoding Of Nanopore-Sequenced Synthetic DNA Storing Digital Images

Autori: Eva Gil San Antonio, Melpomeni Dimopoulou, Marc Antonini, Pascal Barbry, Raja Appuswamy
Pubblicato in: 2021 IEEE International Conference on Image Processing (ICIP), 2021, Pagina/e 1899-1903, ISBN 978-1-6654-4115-5
Editore: IEEE
DOI: 10.1109/icip42928.2021.9506592

A Sequencing Noise Resistant Code Mapping Algorithm for Image Storage in DNA

Autori: Melpomeni Dimopoulou, Eva Gil San Antonio, Marc Antonini
Pubblicato in: CORESA, 2020
Editore: CORESA

Storing Digital Data Into DNA: A Comparative Study Of Quaternary Code Construction

Autori: Melpomeni Dimopoulou, Marc Antonini, Pascal Barbry, Raja Appuswamy
Pubblicato in: ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2020, Pagina/e 4332-4336, ISBN 978-1-5090-6631-5
Editore: IEEE
DOI: 10.1109/icassp40776.2020.9054654

OneJoin: Cross-architecture, scalable edit similarity join for DNA data storage using oneAPI

Autori: Marinelli, Eugenio; Appuswamy, Raja
Pubblicato in: ADMS, 2021
Editore: ADMS

A quaternary code mapping resistant to the sequencing noise for DNA image coding

Autori: Melpomeni Dimopoulou, Eva Gil San Antonio, Marc Antonini
Pubblicato in: MMSP, 2020
Editore: IEEE Xplore

Universal Layout Emulation for Long-Term Database Archival

Autori: Raja Appuswamy, Vincent Joguin
Pubblicato in: Conference on Innovative Data Systems Research, 2021
Editore: Conference on Innovative Data Systems Research (CIDR)

Non-peer reviewed articles (1)

Towards passive, migration-Free, standardized, long-term database archival

Autori: Appuswamy, Raja
Pubblicato in: SIGMOD Record, 2022, ISSN 0163-5808
Editore: Association for Computing Machinary, Inc.
DOI: 10.1145/3552490.3552506

Peer reviewed articles (2)

Direct oligonucleotide sequencing with nanopores

Autori: Sachin Chalapati, Conor A Crosbie, Dixita Limbachiya, Nimesh Pinnamaneni
Pubblicato in: Open Research Europe, Numero 1, 2021, Pagina/e 47, ISSN 2732-5121
Editore: EU Commission
DOI: 10.12688/openreseurope.13578.2

Image storage onto synthetic DNA

Autori: Melpomeni Dimopoulou, Marc Antonini, Pascal Barbry, Raja Appuswamy
Pubblicato in: Signal Processing: Image Communication, Numero 97, 2021, Pagina/e 116331, ISSN 0923-5965
Editore: Elsevier BV
DOI: 10.1016/j.image.2021.116331

Other (1)

Direct oligonucleotide sequencing with nanopores

Autori: Sachin Chalapati, Conor Crosbie, Dixita Limbachiya and Nimesh Chandra Pinnamaneni
Pubblicato in: Protocol Exchange, 2020
Editore: Nature Research
DOI: 10.21203/rs.3.pex-914/v1

Diritti di proprietà intellettuale

Patent (2)

Methods for storing digital data as, and for transforming digital data into, synthetic DNA

Numero candidatura/pubblicazione: 20 2016811985
Data: 2020-03-06
Candidato/i: CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS

Methods for storing digital data as, and for transforming digital data into, synthetic DNA

Numero candidatura/pubblicazione: 20 2016811985
Data: 2020-03-06
Candidato/i: UNIVERSITE DE NICE - SOPHIA ANTIPOLIS