Explore Mosaic and be part of the microbiome community!

As with all systems, Mosaic relies on files to store data. Files can be uploaded from your computer or generated by running apps, and can be shared with the Mosaic community.


    • Import data from SRA database.
    • You can upload small files directly from your web browser by clicking “Add files”.
    • For large files that are accessible over the Internet, we suggest running the “Fetch file from URL” app, which has been provided by the Mosaic team.
    • For large files that are on your computer, we suggest using the Mosaic uploader, a command-line tool capable of uploading with multiple threads and more resilient to transient errors.


Organize Data

  • Workspaces: a venue for data organization, collaboration and analysis.
    • Workspaces act as your own personal hard drive. All data is secure and private unless specifically shared by you.
  • Studies and Runs: organize sequencing data and associated metadata.
  • Search: search metadata from any Workspace, Run, Study, App or Execution that are accessible to the user, including public reference.
  • Public Apps: access preinstalled popular microbiome analysis tools.
    • Metaphlan2
    • MIDAS
    • CLARK
    • Kraken
    • Metaspades
    • IDBA-UD
  • Private Apps: implement your own tools in an easy to access environment.
    • Take a public app or a private app shared with you to make further developments and save it as your own app, a process known as “forking” and inspired from the model of Github repositories.
  • Workflows: chain individual apps in pipelines
  • Execution tracking:  monitor running jobs and access completed executions

with Data

Share Data
and Collaborate

  • Groups: manage collaborating teams.
    • Any user can create and manage a group. The creator of the group is by default an Administrator (admin). Admins may add or remove group participants, or promote them to admins. A user may administer or be a member in an unlimited number of groups, and groups may have an unlimited number of users.
    • Workspaces can be shared with Groups at the same access levels available for users. Each member of the group will have the access level granted to the group, unless the member has been explicitly granted a higher access level.
  • Discussions: a forum to post discussion topics and engage community to juxtapose their answers.
    • A discussion topic functions much like a note, in that it supports rich text formatting and attachments. Under each topic, each participant is allowed to post exactly one answer, also richly formatted and with attachments.
  • Data sharing: control access to data.
    • All data are accessed only by you until you are ready to share with other researchers.
  • Publishing: sharing with the greater Mosaic community.
    • By using publishing, you can contribute reference data, software, results, or pretty much anything else, so that others can use them.
  • Licensing Terms: require acknowledgment of licensing terms to Workspaces, Apps and Assets
  • Licensing Terms (LT) can be attached to App versions, Workspaces and Assets. You can manage your licenses through the license page in your profile. You may use a platform provided platform sample, or create your own LTs.

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