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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/
  • CodaLab (Open Source Team):
  • Federated learning challenge is being built. Initial design:
    Image Added
  • True-CT Challenge
    • Lots of work for making sure participants can securely upload data. Finished now. 
  • DL-SPARSE Challenge
    • Updates to starter kit
    • Updates to load validation data into public directory
  • SIRPRISE Challenge
    • There may be an email bug so working with Diane to iron that out.
    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.
      • Image Removed
      • Image Removed
    • 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_3/31_/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 resourcesInfrastructure is built and now we are editing the template challenge to be the real challenge. 
  • Federated Learning Challenge: 
    • Still need VPN access to environment.
    • Kendall Schmidt (from ACR) and Holger Roth (from NVIDIA) are creating a bash script that kicks off a participant container. 
    • I will be in charge of orchestrating the start of that script from the MedICI website.
  • CodaLab (Open Source Team): 
    • Adding more functionality to the highlights page for the addition of dynamic news.
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.
    3. UPDATE (03_31_2022): The CodaLab (Open Source Team) has updates to the python2 → python3 update branch on github and I think it will work on NCI's network.

MeetingDate
Bi-weekly Meeting #1

 

Bi-weekly Meeting #2

 

Milestones

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

 

Launched SIRPRISE Challenge (https://medici-codalab-main.eastus.cloudapp.azure.com/competitions/22)
Python3 version of CodaLab may be ready for NCI's environment.

11 Feb  

Task in Progress

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

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