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View Code? Open in Web Editor NEWCOVID-19 DREAM Challenge
COVID-19 DREAM Challenge
return {site: "UW",
dataset_name: "uw_omop_covid_q1",
train_dataset_version: "05-06-2020",
infer_dataset_version: "05-06-2020"};
sagebionetworks/synapse-workflow-orchestrator-toil:latest
Pages should be created under
Places that need to be editted for dataset name + dataset version
Currently using a unmerged branch in challengeworkflowtemplate. Use new tagged version once merged.
Catch the prediction file empty exception instead of throwing an error and automatically edit the UW submission status column
https://www.synapse.org/#!Synapse:syn21849256/wiki/601866
Important: Do not post sensitive information about the datasets here (public GitHub repo)
Current if a submission fails internally, the error doesn't always get propagated back.
The datasets that are use in the run_train and run_docker steps must be in docker volumes
FAQ is draft in this Google doc
Add a section on the top of the home page to advertise the latest news.
Remove content and add pointer to useful resources (Justing mentioned a bioRxiv page)
See Challenge Questions.
We will reuse the same server as for the Patient Mortality challenge. Will we get additional servers funded by CD2H or other sources of funding?
Justin mentioned that IBM and X may be interested in helping, but if it's cloud servers UW may not be willing to place EHR data there.
synthetic_omop_covid_q1
05-15-2020
Loop in Hsiao-Ching and Julie (already done) to prepare the press release. Share available material with them.
eval_dataset_name = "uw_omop_covid_eval"
eval_dataset_version = "05-06-2020"
train_dataset_name = "uw_omop_covid_train"
train_dataset_version = "05-06-2020"
Use these values to create the input_dir
in workflow.
During our weekly call on Monday, we will test
Deploy model-to-data configuration on UW site. Start from the configuration used for the EHR DREAM Challenge: Patient Mortality Prediction.
The Home page is drafted here: https://docs.google.com/document/d/1xs0bCEs2nvnd1I-7-wO4QCMS-7hkQiAtTY8louSQ1co/edit?ts=5e83859b#
Changes:
**Description:** {description}
**Ranked features:** {ranked_feature}
**References:** {resources}
{train_name}_{train_version}
{eval_name}_{eval_version}
set to 500
Create a video tutorial similar to the one that we have created for the Metadata Automation DREAM Challenge: https://www.youtube.com/watch?v=YTkocEZfOzs
Ask Verena is she can also make this tutorial
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