The NanoFlow Repository

Authors

Jessie E Arce
Joshua A Welsh
Sean Cook
John Tigges
Ionita Ghiran
Jennifer C Jones
Andrew Jackson
Matthew Roth
Aleksandar Milosavljevic

Publication Date

6-1-2023

Journal

Bioinformatics

DOI

10.1093/bioinformatics/btad368

PMID

37285317

PMCID

PMC10272702

PubMedCentral® Posted Date

6-7-2023

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

Software, Databases, Factual, Flow Cytometry

Abstract

Motivation

Extracellular particles (EPs) are the focus of a rapidly growing area of exploration due to the widespread interest in understanding their roles in health and disease. However, despite the general need for EP data sharing and established community standards for data reporting, no standard repository for EP flow cytometry data captures rigor and minimum reporting standards such as those defined by MIFlowCyt-EV (https://doi.org/10.1080/20013078.2020.1713526). We sought to address this unmet need by developing the NanoFlow Repository.

Results

We have developed The NanoFlow Repository to provide the first implementation of the MIFlowCyt-EV framework.

Availability and implementation

The NanoFlow Repository is freely available and accessible online at https://genboree.org/nano-ui/. Public datasets can be explored and downloaded at https://genboree.org/nano-ui/ld/datasets. The NanoFlow Repository’s backend is built using the Genboree software stack that powers the ClinGen Resource, specifically the Linked Data Hub (LDH), a REST API framework written in Node.js, developed initially to aggregate data within ClinGen (https://ldh.clinicalgenome.org/ldh/ui/about). NanoFlow’s LDH (NanoAPI) is available at https://genboree.org/nano-api/srvc. NanoAPI is supported by a Node.js Genboree authentication and authorization service (GbAuth), a graph database called ArangoDB, and an Apache Pulsar message queue (NanoMQ) to manage data inflows into NanoAPI. The website for NanoFlow Repository is built with Vue.js and Node.js (NanoUI) and supports all major browsers.

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