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

Ken Youens-Clark, Matt Bomhoff, Alise J. Ponsero, Elisha M. Wood-Charlson, Joshua Lynch, Illyoung Choi, John H Hartman, Bonnie L Hurwitz

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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.

Original languageEnglish (US)
JournalGigaScience
Volume8
Issue number7
DOIs
StatePublished - Jul 1 2019

Fingerprint

Microbiota
Agave
Information Dissemination
Information Storage and Retrieval
Computational Biology
Software
HTTP
Datasets
Data integration
Bioinformatics
Metadata
Application programming interfaces (API)
World Wide Web
Containers
Research
Population

Keywords

  • bioinformatics
  • cloud computing
  • cyberinfrastructure
  • metagenomics

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications

Cite this

Youens-Clark, K., Bomhoff, M., Ponsero, A. J., Wood-Charlson, E. M., Lynch, J., Choi, I., ... Hurwitz, B. L. (2019). iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences. GigaScience, 8(7). https://doi.org/10.1093/gigascience/giz083

iMicrobe : Tools and data-dreaiven 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.

In: GigaScience, Vol. 8, No. 7, 01.07.2019.

Research output: Contribution to journalArticle

Youens-Clark K, Bomhoff M, Ponsero AJ, Wood-Charlson EM, Lynch J, Choi I et al. iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences. GigaScience. 2019 Jul 1;8(7). https://doi.org/10.1093/gigascience/giz083
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-dreaiven discovery platform for the microbiome sciences. In: GigaScience. 2019 ; Vol. 8, No. 7.
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