To help benchmark and develop methods that will impact translation of microbiome science into health solutions.

Strains #1 is an untargeted microbiome profiling challenge to characterize the community in a sample down to the strain-level whereas Strains #2 is a targeted profiling challenge whereby we would like to accurately determine if a specific strain (given its genome) is present or absent in the sample.

All the strains and genomes provided as part of the Strains #2 challenge are novel strains and hence they would not be found in any other public databases.

No, all compute and storage for the purpose of the challenge (i.e. occurring in the Workspace created for you when you joined the challenge) is sponsored. It’s FREE to participate!

  • Dynamic

    Participants can submit multiple entries and get immediate results of their performance to allow for further method development. The leaderboard will track of how the challenge is progressing on multiple fronts!

  • Real datasets

    Other challenges have been mostly limited to simulated datasets. Performance on simulated datasets does not translate directly for real datasets. This challenge will comprise two sets of datasets: “Test” and “Challenge”. Test and Challenge datasets will both be comprised of one real metagenome and three simulated metagenomes to ensure methods can be evaluated holistically and robustly.

    Test datasets will be released when the challenge is launched together with the “truth” to help participants refine their methods. Challenge datasets will be used to prevent overtraining of the methods.

  • Reproducible and usable

    All results will be hosted on the Mosaic platform and can be instantly reproduced, and apps on Mosaic can be utilized on other datasets.

  • Progressive

    We do not expect to achieve the perfect solution at the end of this challenge and hence this is the first in a series of profiling challenges that will build on each other towards the level of specificity, sensitivity and resolution needed for the methods needed by industry to translate insights into products.

Emails will be sent to the winners at the email that participants use to create their accounts.

Results will be evaluated after the conclusion of the challenge. Learn more about the evaluation criteria. LINK

Recognition by the community that you have developed an outstanding method! If the challenge leads to publication, there will potentially be additional opportunities for visibility.

Yes, you can submit your results anonymously. However, we keep a record of the identity of the submitter, so we may contact you if we need to. We will not share this information.

No, you do not have to be a U.S. citizen to participate in the challenge or use Mosaic.

Yes, you can become a Mosaic user and participate in the challenge even if you are outside U.S.

The Apps that have been made public during the challenge period will always be available for users to run. Additionally, the Apps that users selected to publish while submitting entries to the Testing Ground or the Challenge will also become public after the end of the challenge.

Yes, we strongly encourage participants to refine and better their performance.

Yes, at submission time, you can select any name you want, yours or team's. This will be visible to other users.

You can associate your app with different licenses to protect your IP. See documentation.

The challenge opens February 12, 2018, and will close on August 3, 2018.

After the challenge closes, we will not allow any new submissions, data uploads or new runs in the participant’s challenge workspace.

No one except yourself until you choose to make it public.

When you submit to the Testing Ground, everyone will be able to see the names and contents of the files you submitted. However, submissions to the Challenge part are hidden until after the end of the challenge.

You must create a free Mosaic account to participate in the challenge.

Your Mosaic account will continue to exist after the challenge closes as you can be a Mosaic user without participating in the challenge, and use your account for future challenges.

Participation in Mosaic Community Challenges is free, unless otherwise noted. You can use your credit to store your own datasets and run your own analyses. Once you have exhausted this credit, you will need to provide your billing contact information, if you would like to continue incurring charges.

We hope to see the challenge catalyzing the performance of methods and lead to publication, which would include all non-anonymous participants.

We have created rich documentation and if you do not find the answer, please file a ticket.

Send us a note at We would love to hear your ideas!

Any company, lab, group or individual can host a challenge on Mosaic!