• First steps into the cloud: Us...

Treffer: First steps into the cloud: Using Amazon data storage and computing with Python notebooks

Title:
First steps into the cloud: Using Amazon data storage and computing with Python notebooks
Authors:
Pollak, Daniel J., Chawla, Gautam, Andreev, Andrey, Prober, David A.
Source:
PLoS ONE, 18(2), Art. No. e0278316, (2023-02)
Publisher Information:
Public Library of Science
Publication Year:
2023
Collection:
Caltech Authors (California Institute of Technology)
Subject Terms:
Multidisciplinary
Document Type:
Fachzeitschrift article in journal/newspaper
Language:
unknown
Relation:
https://doi.org/10.17504/protocols.io.rm7vz3z4xgx1/v1; https://doi.org/10.22002/6ejqf-qm267; https://authors.library.caltech.edu/communities/caltechauthors/; https://doi.org/10.1371/journal.pone.0278316; https://www.ncbi.nlm.nih.gov/pmc/PMC9910747; eprintid:119810
DOI:
10.1371/journal.pone.0278316
Availability:
https://doi.org/10.1371/journal.pone.0278316
https://www.ncbi.nlm.nih.gov/pmc/PMC9910747
Rights:
info:eu-repo/semantics/openAccess ; Other
Accession Number:
edsbas.FAAA6328
Database:
BASE

Weitere Informationen

With the oncoming age of big data, biologists are encountering more use cases for cloud-based computing to streamline data processing and storage. Unfortunately, cloud platforms are difficult to learn, and there are few resources for biologists to demystify them. We have developed a guide for experimental biologists to set up cloud processing on Amazon Web Services to cheaply outsource data processing and storage. Here we provide a guide for setting up a computing environment in the cloud and showcase examples of using Python and Julia programming languages. We present example calcium imaging data in the zebrafish brain and corresponding analysis using suite2p software. Tools for budget and user management are further discussed in the attached protocol. Using this guide, researchers with limited coding experience can get started with cloud-based computing or move existing coding infrastructure into the cloud environment. ; © 2023 Pollak 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. The authors gratefully acknowledge Tom Morrell and Dr. Kristin Briney for support. Many thanks to Justin Bois for instructing course BE/Bi 103b. The authors report the following sources of funding: NIH (R35 NS122172) awarded to DAP, NIH (T32 NS105595) awarded to DJP, and Caltech/Amazon AI4Science Cloud Credits Program grant awarded to DAP. Data Availability: Supporting code and calcium imaging data is available from the Caltech Data repository (doi.org/10.22002/6ejqf-qm267). Experiments involving zebrafish were performed according to the California Institute of Technology Institutional Animal Care and Use Committee (IACUC) guidelines and by the Office of Laboratory Animal Resources at the California Institute of Technology. ; Published - journal.pone.0278316.pdf Supplemental Material - journal.pone.0278316.s001.pdf Supplemental Material - ...