PUBLICATION
First steps into the cloud: Using Amazon data storage and computing with Python notebooks
- Authors
- Pollak, D.J., Chawla, G., Andreev, A., Prober, D.A.
- ID
- ZDB-PUB-230210-28
- Date
- 2023
- Source
- PLoS One 18: e0278316e0278316 (Journal)
- Registered Authors
- Prober, David
- Keywords
- none
- MeSH Terms
-
- Animals
- Cloud Computing
- Information Storage and Retrieval
- Programming Languages
- Software*
- Zebrafish*
- PubMed
- 36757918 Full text @ PLoS One
Citation
Pollak, D.J., Chawla, G., Andreev, A., Prober, D.A. (2023) First steps into the cloud: Using Amazon data storage and computing with Python notebooks. PLoS One. 18:e0278316e0278316.
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping