Challenge Infrastructure | Synapse Documentation

Challenge Infrastructure

This guide is meant to help organizers create a challenge space within Synapse to host a crowd-sourced challenge. A challenge space provides participants with a Project to learn about the challenge, join the challenge community, submit entries, track progress and view results. This document will focus on:

  • Creating the challenge space
  • Launching the challenge space
  • Interacting with the submitted entries

Create the Challenge Space

The following steps are automated by the createchallenge command in the challengeutil python package. The instructions to install and use this package are located in the Challenge Utilities Repository. This guide describes the key Synapse components generated by the tool.

Challenge Projects

The command createchallenge creates two Synapse Projects and initializes the Wiki of the Live challenge Project with a pre-registration page:

  • Live challenge project - The Live challenge Project serves as the pre-registration page during challenge development and is replaced with a challenge Wiki once the challenge is ready to be launched to allow participants to register for the challenge. Organizers fill in the content of the Wiki to provide detailed information about the challenge (e.g. challenge questions, data, participation, evaluation metrics…). The Wiki page must be made public to allow anyone to learn about the challenge and pre-register.

  • Staging challenge project - This Project is used by the organizers during the development of the challenge to share files and draft the challenge Wiki. createchallenge initializes the Wiki with the DREAM Challenge Wiki Template.

Maintence of both a Staging and Live Project enables Wiki content to be edited and previewed in the Staging Project before the content is published to the Live challenge Project.

Important: All edits and changes should be made on the Staging site.

For background on how to create and share Projects, Files, Folders and Wiki pages, please see our article Making a Project.

Synapse Teams

The command createchallenge creates three Synapse Teams:

  • Challenge participant team - This Synapse Team includes the individual participants and Teams that register to the challenge.

  • Challenge administrator team - The challenge organizers must be added to this list to provide the permissions to share files and edit the content of the Wiki on the Staging Project.

  • Challenge pre-registration team - This Team is recommended for when the challenge is under development. It allows participants to join a mailing list to receive notification of challenge launch news.

Please visit this page to learn more about Teams.

Activating Challenge Configuration

The command createchallenge also connects the challenge participant team to the Live challenge Project to effectively enable participant submissions.

Upload Challenge Data

The challenge data (e.g. training dataset, scoring data…) are uploaded to the Live challenge Project when it is ready to be shared with participants.

For background on how to create and share Project, Files, Folders and Wiki pages, please see our article Making a Project.

Adding Conditions for Use

Synapse has the ability to apply access restrictions to sensitive data (e.g. human data), so that legal requirements are met before participants access such data. If human data are being used in the challenge, or if you have any question about the sensitivity of the challenge data, please contact the Synapse Access and Compliance Team ( for support to ensure that the necessary data access approval procedures are put in place.

There are cases where there are no human data concerns and instead a pop-up agreement needs to be presented before the first data download. Contact the Access and Compliance Team to set up this agreement.

Please view the Access Controls page to learn how to add conditions for use on data.

Create an Evaluation Queue for Submissions

Challenge participants can submit Synapse Entities (e.g. File, Folder, Project, Docker) to evaluation queues. Multiple Evaluation queues can be created to support challenges with more than one question.

Please visit the Evaluation Queue article to learn more about queue configuration.

One of the features of Synapse for DREAM Challenges is the live compilation of submission statistics for all evaluation queues, including total submission count, count per individual/team, count per submission state (scored, invalid) and count per week. You can see the statistics for various challenges here. In order to activate statistics for your evaluation queues, you must be an administrator of the challenge Project. Each queue needs to be configured to generate the statistics. To do this:

  1. Navigate to your Challenge project in Synapse.
  2. Click on the Challenge tab.
  3. Next to each Evaluation submission queue, click Share.
  4. In the name field type evaluationstatistics. The new entry will appear in the list of accessors above.
  5. Next to the new entry use the pull down menu to change Can View to Can Score.
  6. Click Save.

Statistics are updated weekly. They are also retroactive - you do not have to enable statistics at the beginning of your challenge to have the entire history reported.

Launch the Challenge Space

To launch the space, share the evaluation queues with the participant Team and use the copyWiki command provided by synapseutils to deploy the initial Staging Wiki to the Live challenge Project. The Wiki of the Live Project will then be replaced by the Wiki in the Staging Project.

After the initial deployment, the mirrorwiki command provided by challengeutils mirrors the Wiki from the Staging site to the Live site throughout the duration of the challenge. The Wiki titles must match to maintain this connection.

Interacting with Submissions

Throughout the challenge, participants will continuously submit to the evaluation queues. To manage continuous submissions, organizers can automate validation and scoring with the Synapse python client evaluation commands.

Revealing Submissions and Scores

Organizers can create leaderboards when scores are ready to be revealed to participants using Submission Views.

Submission views are sorted, paginated, tabular forms that can display submission data and annotations (e.g. scores from the scoring application and other metadata) and update as annotations or scores change. A submission view can provide real-time insight into the progress of a challenge.

Learn more about adding leaderboards in the Evaluation Queue article.

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