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Activities completed this month

  • MIDRC is up and running and challenge details are being ironed out: http://midrc-medici-competitions.eastus.cloudapp.azure.com/
  • Tested new github commits to the codalab framework code. They have merged in code that was porting the proiect to python3 (previously I was doing this on my own). It still has some issues. Will keep monitoring it so we can get an updated codalab base for our projects.
    • UPDATE (1_07_2022): I emailed the codalab team asking for updates regarding the python3 port of the old codalab. I also asked about their future project codabench. They informed me that they are working on both but the python3 port for now (as they have a small team). They offered me a chance to join the meetings and perhaps help. I will join their Monday\Thursday calls to catch and see if and how I can help.
    • UPDATE (1_31_2022): Need to work on github workflows in order to have my changes allowed into the codalab system. 
    • UPDATE (2_28_2022): I managed to get circleci (the current testing system) to work and even updated some of their code to update the way it is used. We will stick with this.
      • Also I tested the hello world competition on https://www.codabench.org/ and the first submission fails but the second works. They are aware but consider it a low priority issue.
    • Launching Emil's Challenge shortly and still working on the scoring program and data access for users. The planned release date is 3/17/2022.
Planned for next month
  • MIDRC Challenge 0 which will feature docker submissions as well as the Image Comparator app and a jupyter notebook for annotator analysis. - Still waiting on credits for Azure use.
    • UPDATE (01_31_2022): we have credits but again now we need a risk assessment for Partners IT to accept this set of credits.
    • UPDATE (02_28_2022): submitted the risk assessment but still no word on resources
Paused
  1. Continue getting CodaLab running on NCI's network and VMs:
    1. Issues:
      1. Credentials for AWS bucket not active and we cannot talk to the bucket. Need to reach out to Tony Bigham (tony.bigham@nih.gov) to get those refreshed. 
      2. On my local machine I deployed the updated CodaLab code and tried connecting to my own S3 bucket instance. I noticed that there is a javascript error making the request to the bucket. I need to setup up a similar but more simple setup to figure out how to upload data to s3 via javascript http requests so that I can trouble shoot the error on NCI's system and or mine. If we could use Azure, this might be resolved.
    2. UPDATE (01_31_2022): May have a work around with a storage service called MINIO.

MeetingDate
Bi-weekly Meeting #1

 

Bi-weekly Meeting #2

 

Milestones

DescriptionDate
Launched TrueCT Challenge (https://medici-codalab-main.eastus.cloudapp.azure.com/competitions/23)

 

Launched SIRPRISE Challenge (https://medici-codalab-main.eastus.cloudapp.azure.com/competitions/22)

 

Task in Progress

Description
Launching DL-Sparse Challenge from Emil soon. This is version 2.

Risks

Description

Mitigation

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Realization

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