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Activities completed this month

  • The BMMR2: Breast Multiparametric MRI for prediction of NAC Response challenge is over and has 8 submissions. Closes submissions as Dr. Newitt doesn't want to share the data as of now. 
    • In January I've been collecting stats on:
      • Total submissions in each phase by participant.
      • Who participated in the Test\Retest portion of the challenge.
    • There were some late submissions that we wanted to make sure weren't too late to be allowed in the system.
    • We also found a participant who never put their submission on the leaderboard but still wanted to participate so we had to manually add them.


  • MIDRC:
    • Azure credits have come through but we have to create a risk assessment in Partners for Azure use.
      • This may take too long so while I will fill this out I need to maybe launch a version of this on Jayashree's Azure account to get this moving. 
  • DAIR Digital Breast Tomosynthesis Cancer Detection Challenge - Phase 2 (DBTex2) - Dr. Mateusz Buda has reached out about a potential data problem for the test phase. I have send the code and data I used and we are working to make sure the challenge results from participants are accurate.Will be in touch with him over the next couple days to make sure everything is in order. 
    • UPDATE (01_07_2022):Sent a follow up email. Not sure what the resolution is so far
  • 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 hlephelp.
    • UPDATE (1_31_2022): Need to work on github workflows in order to have my changes allowed into the codalab system. 
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_0731_2022): no credits
  • Jayashree has me collaborating with Steve Piper (sponsored collaborator) who has built a way to make OHIF (medical imaging viewer) talk to a database called couchdb. This is a nosql record style database that the app I'm buillding for MIDRC is based on. The plan is to integrate OHIF into this app and be able to launch beside codalab and MedICI in general. This would allow ePAD and caMicroscope like functionality with more flexibility as well. Progress on this will come soon as I dive in.
    • UPDATE (01_07_2022): Haven't started
  • Figure out how to add a phase to a challenge (SPIE specifically with Dr. Mazurowski but maybe others as well).
    • UPDATE (01_07_2022): Turns out the button to add a phase was commented out and luckily un commenting it added the functionality back in!
  • Re secure DL Sparse certificate
    • UPDATE (01_07_2022): Done as well as other sites that needed it
  • Emailed Dr. Bilal Tahir regarding if he wants his challenge open: http://aapmchallenges.cloudapp.net/competitions/35. Awaiting reply.
    • we have credits but again now we need a risk assessment for Partners IT to accept this sset of credits.
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_0731_2022): Isabelle Guyon of chalearn.org has invited me to some zoom meetings with the maintainers of codalab. I will try to help bring codalab into the python3 future and help us to have a solid foundation for MedICI custom features as well as have code that might pass NCI inspection on the security sideMay have a work around with a storage service called MINIO.

MeetingDate
Bi-weekly Meeting #1

 

Bi-weekly Meeting #2

 

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