Deliverables
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 HybridisationThis 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 TechniquesThis 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 protocolsThis 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
Publications
Author(s):
E. Gil San Antonio, T. Heinis, L. Carteron, M. Dimopoulou and M. Antonini
Published in:
VCIP 2021, 2021
Publisher:
IEEE
DOI:
10.1109/vcip53242.2021.9675388
Author(s):
X. Pic, M. Antonini
Published in:
EUSIPCO 2022, 2022
Publisher:
IEEE
DOI:
10.23919/eusipco55093.2022.9909833
Author(s):
Eugenio Marinelli, Eddy Ghabach, Thomas Bolbroe, Omer Sella, Thomas Heinis and Raja Appuswamy
Published in:
iPRES 2021, 17th International Conference on Digital Preservation, 2021
Publisher:
N/A
Author(s):
Melpomeni Dimopoulou, Marc Antonini
Published in:
2020 Data Compression Conference (DCC), 2020, Page(s) 363-363, ISBN 978-1-7281-6457-1
Publisher:
IEEE
DOI:
10.1109/dcc47342.2020.00085
Author(s):
Eva Gil San Antonio; Mattia Piretti; Melpomeni Dimopoulou; Marc Antonini
Published in:
https://hal.archives-ouvertes.fr/hal-03100971, Issue 2, 2020
Publisher:
IEEE
DOI:
10.1109/icpr48806.2021.9411920
Author(s):
Melpomeni Dimopoulou, Marc Antonini
Published in:
EUSIPCO, 2020
Publisher:
EURASIP
Author(s):
Marinelli, Eugenio; Appuswamy, Raja
Published in:
DAMON, 2021
Publisher:
ACM
Author(s):
Eugenio Marinelli, Eddy Ghabach, Thomas Bolbroe, Omer Sella, Thomas Heinis and Raja Appuswamy
Published in:
BDA 2021, 37ème Conférence sur la Gestion de Données – Principles, Technologies et Applications, 2021
Publisher:
N/A
Author(s):
Dimopoulou, Melpomeni; GIl, Eva; Antonini, Marc
Published in:
EUSIPCO 2021, IEEE, 2021
Publisher:
IEEE
Author(s):
Yiqing Yan; Nimisha Chaturvedi; Raja Appuswamy
Published in:
IPDPSW 2022, 2022
Publisher:
IEEE
DOI:
10.1109/ipdpsw55747.2022.00036
Author(s):
Eva Gil San Antonio, Melpomeni Dimopoulou, Marc Antonini, Pascal Barbry, Raja Appuswamy
Published in:
2021 IEEE International Conference on Image Processing (ICIP), 2021, Page(s) 1899-1903, ISBN 978-1-6654-4115-5
Publisher:
IEEE
DOI:
10.1109/icip42928.2021.9506592
Author(s):
Melpomeni Dimopoulou, Eva Gil San Antonio, Marc Antonini
Published in:
CORESA, 2020
Publisher:
CORESA
Author(s):
Melpomeni Dimopoulou, Marc Antonini, Pascal Barbry, Raja Appuswamy
Published in:
ICASSP 2020 - 2020 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2020, Page(s) 4332-4336, ISBN 978-1-5090-6631-5
Publisher:
IEEE
DOI:
10.1109/icassp40776.2020.9054654
Author(s):
Marinelli, Eugenio; Appuswamy, Raja
Published in:
ADMS, 2021
Publisher:
ADMS
Author(s):
Melpomeni Dimopoulou, Eva Gil San Antonio, Marc Antonini
Published in:
MMSP, 2020
Publisher:
IEEE Xplore
Author(s):
Raja Appuswamy, Vincent Joguin
Published in:
Conference on Innovative Data Systems Research, 2021
Publisher:
Conference on Innovative Data Systems Research (CIDR)
Author(s):
Sachin Chalapati, Conor A Crosbie, Dixita Limbachiya, Nimesh Pinnamaneni
Published in:
Open Research Europe, Issue 1, 2021, Page(s) 47, ISSN 2732-5121
Publisher:
EU Commission
DOI:
10.12688/openreseurope.13578.2
Author(s):
Melpomeni Dimopoulou, Marc Antonini, Pascal Barbry, Raja Appuswamy
Published in:
Signal Processing: Image Communication, Issue 97, 2021, Page(s) 116331, ISSN 0923-5965
Publisher:
Elsevier BV
DOI:
10.1016/j.image.2021.116331
Author(s):
Sachin Chalapati, Conor Crosbie, Dixita Limbachiya and Nimesh Chandra Pinnamaneni
Published in:
Protocol Exchange, 2020
Publisher:
Nature Research
DOI:
10.21203/rs.3.pex-914/v1
Intellectual Property Rights
Application/Publication number:
20
2016811985
Date:
2020-03-06
Applicant(s):
UNIVERSITE DE NICE - SOPHIA ANTIPOLIS
Application/Publication number:
20
2016811985
Date:
2020-03-06
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