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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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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 |
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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 |
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