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

Dataset type: Software, Workflow
Data released on June 19, 2019

Youens-Clark K; Bomhoff M; Ponsero A; Wood-Charlson EM; Lynch J; Choi I; Hartman JH; Hurwitz BL (2019): Supporting data for "iMicrobe: Tools and data-driven discovery platform for the microbiome sciences" GigaScience Database.


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 hasn’t been fully realized given that the tools, data sets, and computation are available in diverse repositories and locations. To address this challenge, we developed, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community.
The iMicrobe platform brings together analysis tools and microbiome data sets 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).
iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a webbased platform.

File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive363.46 KB2019-06-12
GitHub archivearchive58.22 KB2019-06-12
ReadmeTEXT2.91 KB2019-06-19
Displaying 1-3 of 3 File(s).
Funding body Awardee Award ID Comments
Gordon and Betty Moore Foundation B Hurwitz 4491
National Science Foundation K Youens-Clark 1639588
Simons Foundation B Hurwitz SCOPE
Date Action
June 19, 2019 Dataset publish
June 24, 2019 Manuscript Link added : 10.1093/gigascience/giz083
August 31, 2019 Manuscript Link added : 10.1093/gigascience/giz097
October 14, 2022 Manuscript Link updated : 10.1093/gigascience/giz083
October 14, 2022 Manuscript Link updated : 10.1093/gigascience/giz097