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.

doi:10.1093/gigascience/giz083

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

Journal Article · 09 July 2019 · GigaScience

DOI: https://doi.org/10.1093/gigascience/giz083 · OSTI ID:1625348

^[1]; Bomhoff, Matt ^[2]; Ponsero, Alise J. ^[2]; Wood-Charlson, Elisha M. ^[3]; Lynch, Joshua ^[2]; Choi, Illyoung ^[4]; Hartman, John H. ^[4];

^[5]

Univ. of Arizona, Tucson, AZ (United States). Dept. of Biosystems Engineering; DOE/OSTI
Univ. of Arizona, Tucson, AZ (United States). Dept. of Biosystems Engineering
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
Univ. of Arizona, Tucson, AZ (United States). Dept. of Computer Science
Univ. of Arizona, Tucson, AZ (United States). Dept. of Biosystems Engineering; Univ. of Arizona, Tucson, AZ (United States). BIO5 Inst.

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625348

Journal Information:: GigaScience, Journal Name: GigaScience Journal Issue: 7 Vol. 8; ISSN 2047-217X

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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