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Activities completed this month
Demo docker submissions to Emily Townley who is designing a MIDRC challenge. I should have a non-gpu and a gpu submission ready soon Status: Deploy GPU VM through DTI subscription - COMPLETE Test out submissions and have MIDRC folks test them as well - COMPLETE Make some changes to UX workflow for dockersubmimssions - 99% COMPLETE. Debugging final deployment issue Kheops report is finalized and we just received word from Joel (from Kheops) that OHIF only saves length measurements. I will add that detail to the report and hand off to Ulli. - COMPLETE Didn't quite get around to fixing the codalab deployment on nci's network. A docker issue crept up again and I had to wait for Kevin Olexa to disable "cylancecsv", some sort of anti-virus software. UPDATE 1: We have fixed a server issue with Apache that wasn't allowing css and js files to be served to the front end. UPDATE 2: We have a new issue where specific AWS js files related to container storage are not being served and it's causing competition upload to stall and not complete as data cannot be communicated to AWS. We were able to see Kendall from ACR and deploy the DMIST data on 3 clients and 1 server. The basic setup works. I need to replicate this on azure credits we have that are being provisioned (We have them but are undergoing a security check before resources are provisioned). In the meantime there is a tutorial I need to do better understand the framework, but I have a good general flow for now. Put DBTEX2 on medici-challenges.
Fixed the server issue. Apache was watching the wrong directory Set up my own AWS S3 bucket and was able to talk to it with a terminal CLI (aws cli)

Activities completed this month

Demo docker submissions to Emily Townley who is designing a MIDRC challenge. I should have a non-gpu and a gpu submission ready soon
1. Status:
  1. Deploy GPU VM through DTI subscription - COMPLETE
  2. Test out submissions and have MIDRC folks test them as well - COMPLETE
  3. Make some changes to UX workflow for dockersubmimssions - 99% COMPLETE. Debugging final deployment issue
Kheops report is finalized and we just received word from Joel (from Kheops) that OHIF only saves length measurements. I will add that detail to the report and hand off to Ulli. - COMPLETE
Didn't quite get around to fixing the codalab deployment on nci's network. A docker issue crept up again and I had to wait for Kevin Olexa to disable "cylancecsv", some sort of anti-virus software.
1. UPDATE 1: We have fixed a server issue with Apache that wasn't allowing css and js files to be served to the front end.
2. UPDATE 2: We have a new issue where specific AWS js files related to container storage are not being served and it's causing competition upload to stall and not complete as data cannot be communicated to AWS.
We were able to see Kendall from ACR and deploy the DMIST data on 3 clients and 1 server. The basic setup works. I need to replicate this on azure credits we have that are being provisioned (We have them but are undergoing a security check before resources are provisioned). In the meantime there is a tutorial I need to do better understand the framework, but I have a good general flow for now.
Put DBTEX2 on medici-challenges.

Fixed the server issue. Apache was watching the wrong directory
Set up my own AWS S3 bucket and was able to talk to it with a terminal CLI (aws cli)

Planned for next month
ONGOING - Continue the Federated Learning Document about integrating MedICI and Federated Challenges. Document is pending some additional notes. We are currently working with ACR (American College of Radiology) to deploy some Federated Learning clients and servers and this will greatly help me understand the complexities involved with setting up Federated learning challenges. Next month hopefully I'll have a better idea of what goes into setting up a system like this. Submit an ePoster to AAPM by the end of June. Continue getting CodaLab running on NCI's network and VMs: Issues: 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. 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. Add DAIR challenge (Dr. Mazurowski's challenge part 2) to https://medici-challenges.org

Planned for next month

ONGOING - Continue the Federated Learning Document about integrating MedICI and Federated Challenges.
1. Document is pending some additional notes. We are currently working with ACR (American College of Radiology) to deploy some Federated Learning clients and servers and this will greatly help me understand the complexities involved with setting up Federated learning challenges. Next month hopefully I'll have a better idea of what goes into setting up a system like this.
Submit an ePoster to AAPM by the end of June.
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.
Add DAIR challenge (Dr. Mazurowski's challenge part 2) to https://medici-challenges.org

Meeting	Date
Bi-weekly Meeting #1	10 Jun 05 Aug 2021
Bi-weekly Meeting #2	24 Jun 19 Aug 2021

Milestones

Description	Date
Got CodaLab to launch and the UI works at NCI!	22 Jun 2021
We have a server issue where changes to CSS and Javascript files aren't being reflected in the browser.	30 Jul 2021

Task in Progress

Description	Status	Creation Date	Close Date
Deployment of CodaLab on NCI's network	In Progress	01 Jul 2021
Troubleshooting a javascript http request to Amazon AWS S3 bucket	In Progress	31 Aug 2021

Risks

Description	Mitigation	Rank	Status	Creation Date	Realization	Close Date
Continuous development of CodaLab on NCI's network is exposing bugs in deployment and or CodaLab itself. This isn't an issue in theory, but I don't know how many issues I'll need to correct in order for the system to work. It is hard to estimate time to completion as a consequence.	Kevin Olexa and I are working together to address each as they come up.	1	In Progress	23 Jul 2021

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