Cargando…

iMicrobe: Tools and data-driven discovery platform for the microbiome sciences

BACKGROUND: 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 rep...

Descripción completa

Detalles Bibliográficos
Autores principales: Youens-Clark, Ken, Bomhoff, Matt, Ponsero, Alise J, Wood-Charlson, Elisha M, Lynch, Joshua, Choi, Illyoung, Hartman, John H, Hurwitz, Bonnie L
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6615980/
https://www.ncbi.nlm.nih.gov/pubmed/31289831
http://dx.doi.org/10.1093/gigascience/giz083
_version_ 1783433427909869568
author Youens-Clark, Ken
Bomhoff, Matt
Ponsero, Alise J
Wood-Charlson, Elisha M
Lynch, Joshua
Choi, Illyoung
Hartman, John H
Hurwitz, Bonnie L
author_facet Youens-Clark, Ken
Bomhoff, Matt
Ponsero, Alise J
Wood-Charlson, Elisha M
Lynch, Joshua
Choi, Illyoung
Hartman, John H
Hurwitz, Bonnie L
author_sort Youens-Clark, Ken
collection PubMed
description BACKGROUND: 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.
format Online
Article
Text
id pubmed-6615980
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-66159802019-07-15 iMicrobe: Tools and data-driven discovery platform for the microbiome sciences Youens-Clark, Ken Bomhoff, Matt Ponsero, Alise J Wood-Charlson, Elisha M Lynch, Joshua Choi, Illyoung Hartman, John H Hurwitz, Bonnie L Gigascience Technical Note BACKGROUND: 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. Oxford University Press 2019-07-09 /pmc/articles/PMC6615980/ /pubmed/31289831 http://dx.doi.org/10.1093/gigascience/giz083 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ 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.
spellingShingle Technical Note
Youens-Clark, Ken
Bomhoff, Matt
Ponsero, Alise J
Wood-Charlson, Elisha M
Lynch, Joshua
Choi, Illyoung
Hartman, John H
Hurwitz, Bonnie L
iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
title iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
title_full iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
title_fullStr iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
title_full_unstemmed iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
title_short iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
title_sort imicrobe: tools and data-driven discovery platform for the microbiome sciences
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6615980/
https://www.ncbi.nlm.nih.gov/pubmed/31289831
http://dx.doi.org/10.1093/gigascience/giz083
work_keys_str_mv AT youensclarkken imicrobetoolsanddatadrivendiscoveryplatformforthemicrobiomesciences
AT bomhoffmatt imicrobetoolsanddatadrivendiscoveryplatformforthemicrobiomesciences
AT ponseroalisej imicrobetoolsanddatadrivendiscoveryplatformforthemicrobiomesciences
AT woodcharlsonelisham imicrobetoolsanddatadrivendiscoveryplatformforthemicrobiomesciences
AT lynchjoshua imicrobetoolsanddatadrivendiscoveryplatformforthemicrobiomesciences
AT choiillyoung imicrobetoolsanddatadrivendiscoveryplatformforthemicrobiomesciences
AT hartmanjohnh imicrobetoolsanddatadrivendiscoveryplatformforthemicrobiomesciences
AT hurwitzbonniel imicrobetoolsanddatadrivendiscoveryplatformforthemicrobiomesciences