This guide helps organizers create a space within Synapse to host a crowd-sourced Challenge. Challenges are community competitions designed to crowd-source new computational methods for fundamental questions in systems biology and translational medicine. Learn more about Challenges and see examples of past and current projects by visiting Challenges and Benchmarking.
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This file will be what links the evaluation queue to the orchestrator. Make note of this File ID for use later in Step 10. |
7. /wiki/spaces/DOCS/pages/2667708522 Add an annotation to the file called ROOT_TEMPLATE by clicking on Files Tools > Annotations > Edit. The "Value" will be the path to the workflow script, written as:
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8. Create a cloud compute environment with the required memory and volume specifications, then SSH into the instance.
If you are a Sage employee: you can follow our internal instructions on /wiki/spaces/CHAL/pages/2806087732 here.
If you are not a Sage employee: follow the instructions listed under "Setting up linux environment" to install and run Docker as well as
docker-composeonto the compute environment of choice.
9. On the instance, clone the SynapseWorkflowOrchestrator repo if needed. Change directories to SynapseWorkflowOrchestrator/ and create a copy of the .envTemplate file as .env (or simply rename it to .env):
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When using copyWiki, it is important to specify the destinationSubPageId parameter. This ID can be found in the URL of the live site, where it is the integer following .../wiki/<some number>.
Once copyWiki has been used once, DO NOT USE IT AGAIN!!
Following this action, all changes to the live site should now be synced over with challengeutils' mirrow-wiki. More on updating the Wikis under the Update the Challenge section below.
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Column Name | Description | Facet values? |
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| Evaluation ID (evaluation ID, but rendered as evaluation name) – recommended for SubmissionViews with multiple queues in scope |
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| Submission ID | |
| Date and time of the submission (in Epoch, but rendered as | |
| User or team who submitted (user or team ID, but rendered as username or team name) |
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| Docker image name – recommended for model-to-data challenges |
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| Docker SHA digest – recommended for model-to-data challenges |
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| Workflow status of the submission (one of [ |
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| Evaluation status of the submission (one of [None, |
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| (if any) Validation errors for the predictions file |
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| Synapse ID to the submission’s logs folder |
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| Synapse ID to the predictions file (if any) |
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(any annotations related to scores) | Submission annotations - names used depends on what annotations were used in the scoring step of the workflow |
Recommended
Not recommended...