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ETDB-Caltech: a blockchain-based distributed public database for electron tomography

Ortega, Davi R. and Oikonomou, Catherine M. and Ding, H. Jane and Rees-Lee, Prudence and Jensen, Grant J. (2019) ETDB-Caltech: a blockchain-based distributed public database for electron tomography. PLoS ONE, 14 (4). Art. No. e0215531. ISSN 1932-6203. http://resolver.caltech.edu/CaltechAUTHORS:20181029-160304278

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Abstract

Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1371/journal.pone.0215531DOIArticle
https://doi.org/10.1101/453662DOIDiscussion Paper
ORCID:
AuthorORCID
Ortega, Davi R.0000-0002-8344-2335
Oikonomou, Catherine M.0000-0003-2312-4746
Jensen, Grant J.0000-0003-1556-4864
Additional Information:© 2019 Ortega et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Received: October 17, 2018; Accepted: April 3, 2019; Published: April 15, 2019. We thank members of the Jensen lab for helpful comments on the ETDB interface, as well as past and present lab members (Morgan Beeby, Ariane Briegel, Yi-Wei Chang, Songye Chen, Megan Dobro, Lu Gan, Gregory Henderson, Cristina Iancu, Andreas Kjær, Zhuo Li, Alasdair McDowall, Gavin Murphy, Martin Pilhofer, Rasika Ramdasi, Jian Shi, Poorna Subramanian, Matthew Swulius, William Tivol, Elitza Tocheva, Cora Woodward, Qing Yao, Zhiheng Yu, and Elizabeth Wright) who generously allowed data they collected to be made public. We also thank other lab members whose data will be published in the future. The Alexandria team is composed of Devon Read James, Amy James, Jeremiah Buddenhagen, Sky Young, Ryan Chacon, Joseph Fiscella and Anthony Stewart. Thanks also to past Alexandria contributors Ryan Jordan, Robert English and Ryan Taylor for their work on the Open Index Protocol specification. This work was supported by grants to GJJ from the National Institute of General Medical Sciences (R35 GM122588) and the John Templeton Foundation as part of the Boundaries of Life Project (51250). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Data Availability: All relevant data are within the manuscript, Supporting Information files, and on Github at the following links: https://github.com/theJensenLab/go-etdb https://github.com/theJensenLab/etdb-downloads/blob/master/userManual.md https://github.com/oipwg/oip-js https://github.com/floblockchain/flo https://github.com/theJensenLab/etdb-react. Competing interests: Alexandria and its contributors hold various cryptocurrency tokens, including FLO. DRO and Alexandria contributed to FLO blockchain development.
Funders:
Funding AgencyGrant Number
NIHR35 GM122588
John Templeton Foundation51250
Record Number:CaltechAUTHORS:20181029-160304278
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20181029-160304278
Official Citation:Ortega DR, Oikonomou CM, Ding HJ, Rees-Lee P, Alexandria, Jensen GJ (2019) ETDB-Caltech: A blockchain-based distributed public database for electron tomography. PLoS ONE 14(4): e0215531. https://doi.org/10.1371/journal.pone.0215531
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90481
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:30 Oct 2018 01:41
Last Modified:23 Apr 2019 21:02

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