iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences
Ponsero, Alise J
Wood-Charlson, Elisha M
Hartman, John H
Hurwitz, Bonnie L
AffiliationUniv Arizona, Dept Biosyst Engn
Univ Arizona, Dept Comp Sci
Univ Arizona, BIO5 Inst
MetadataShow full item record
PublisherOXFORD UNIV PRESS
CitationKen Youens-Clark, Matt Bomhoff, Alise J Ponsero, Elisha M Wood-Charlson, Joshua Lynch, Illyoung Choi, John H Hartman, Bonnie L Hurwitz, iMicrobe: Tools and data-driven discovery platform for the microbiome sciences, GigaScience, Volume 8, Issue 7, July 2019, giz083, https://doi.org/10.1093/gigascience/giz083
RightsCopyright © The Author(s) 2019. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Collection InformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at email@example.com.
AbstractBackground: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe. us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community. Findings: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation-supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP). Conclusions: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.
NoteOpen access journal
VersionFinal published version
SponsorsGordon and Betty Moore Foundation's Marine Microbial Initiativegrant ; National Science Foundation ; Simons Foundation's SCOPE project (Simons Collaboration on Ocean Processes and Ecology)
- Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.
- Authors: Choi I, Ponsero AJ, Bomhoff M, Youens-Clark K, Hartman JH, Hurwitz BL
- Issue date: 2019 Feb 1
- fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool.
- Authors: Hubbard A, Bomhoff M, Schmidt CJ
- Issue date: 2020
- gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.
- Authors: Shi W, Qi H, Sun Q, Fan G, Liu S, Wang J, Zhu B, Liu H, Zhao F, Wang X, Hu X, Li W, Liu J, Tian Y, Wu L, Ma J
- Issue date: 2019 Jan 8
- Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis.
- Authors: Weber N, Liou D, Dommer J, MacMenamin P, Quiñones M, Misner I, Oler AJ, Wan J, Kim L, Coakley McCarthy M, Ezeji S, Noble K, Hurt DE
- Issue date: 2018 Apr 15
- COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets.
- Authors: Bose T, Haque MM, Reddy C, Mande SS
- Issue date: 2015