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

Abstract

Abstract BackgroundScientists 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. FindingsThe 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). ConclusionsiMicrobe promotes data integration, sharing, and community-driven tool development by making open source datamore » and tools accessible to the research community in a web-based platform.« less

Authors:
ORCiD logo [1];  [1];  [1];  [2];  [1];  [3];  [3]; ORCiD logo [4]
  1. Univ. of Arizona, Tucson, AZ (United States). Dept. of Biosystems Engineering
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  3. Univ. of Arizona, Tucson, AZ (United States). Dept. of Computer Science
  4. Univ. of Arizona, Tucson, AZ (United States). Dept. of Biosystems Engineering; Univ. of Arizona, Tucson, AZ (United States). BIO5 Inst.
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1625348
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
GigaScience
Additional Journal Information:
Journal Volume: 8; Journal Issue: 7; Journal ID: ISSN 2047-217X
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Life Sciences & Biomedicine - Other Topics; Science & Technology - Other Topics; cyberinfrastructure; cloud computing; bioinformatics; metagenomics

Citation Formats

Youens-Clark, Ken, Bomhoff, Matt, Ponsero, Alise J., Wood-Charlson, Elisha M., Lynch, Joshua, Choi, Illyoung, Hartman, John H., and Hurwitz, Bonnie L.. iMicrobe: Tools and data-driven discovery platform for the microbiome sciences. United States: N. p., 2019. Web. 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-driven discovery platform for the microbiome sciences. United States. 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., and Hurwitz, Bonnie L.. Mon . "iMicrobe: Tools and data-driven discovery platform for the microbiome sciences". United States. https://doi.org/10.1093/gigascience/giz083. https://www.osti.gov/servlets/purl/1625348.
@article{osti_1625348,
title = {iMicrobe: Tools and data-driven discovery platform for the microbiome sciences},
author = {Youens-Clark, Ken and Bomhoff, Matt and Ponsero, Alise J. and Wood-Charlson, Elisha M. and Lynch, Joshua and Choi, Illyoung and Hartman, John H. and Hurwitz, Bonnie L.},
abstractNote = {Abstract BackgroundScientists 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. FindingsThe 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). ConclusionsiMicrobe 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.},
doi = {10.1093/gigascience/giz083},
journal = {GigaScience},
number = 7,
volume = 8,
place = {United States},
year = {2019},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Figures / Tables:

Figure 1 Figure 1: iMicrobe’s architecture allows for the integration of datasets hosted by iMicrobe that can be placed into the data cart, those private to the user, and others publicly accessible on the Internet. Analyses created by iMicrobe or other developers run on Stampede2, and the results go into the user’smore » home directory in the CyVerse Data Store.« less

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      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.