Remaining analyses before writing the paper

[gwaybio]

A note from Adi on the remaining analyses required for a paper:

• Building the bortezomib sensitivity signature
  • Cell line selection and clone generation
  • Any quality control analysis that went into this
  • Generating the Bz signature (WT clones 1-5, BZ clones A, E, 1-5)
  • Applying the Bz signature to other WT (10, 12-15) and Bz-resistant (6-10) clones to see that it applies well to clones the signature wasn't trained on.
• Applying the Bz signature to Ixazomib resistant clones
  • expectation: signature should pick up Ixazomib resistant clones somewhat, but not be a perfect fit
• Applying the Bz signature to CB-5083 resistant clones
  • expectation: signature should pick up CB-5083 resistant clones somewhat, but fit should be similar or worse than Ixazomib

[gwaybio]

cc @ayberman @mekelley

I chatted with @yhan8 yesterday, and she is eager to get started! I let her know that September is a good month for the two of you to dedicate to writing the paper. We walked through generating the new batch profiles (now added in #109) and I've completed QC (added in #106).

@yhan8 approach will be to reproduce the existing analyses by:

1. Creating the conda environment as specified in environment.yml
2. Rerunning the signature generation, evaluation, and visualization in all notebooks provided in the 3.resistance-signature/ folder
3. Tackling these questions above

I suspect that September 1st is going to be quite difficult to complete these three analyses as specified above, especially while trying to get up to speed in a completely new data type. @yhan8, please let us know if you have any questions or concerns, as you make progress towards this goal!

Megan and Adi, I think it will also be wise to think a bit about how to use the September writing block if Yu is able to partially answer the three remaining analyses (not complete).

[yhan8]

Hi All, I am super excited to be added to this project! I just started last week, I am still in the process of setting up Github etc, which I suspect will be done in the next day or two, once that is done, I will reproduce the existing results of Greg's, and move to understand and run the additional analyses. I do agree with Greg that the first week of September is too tight for me, I would target a mid~late September for completed results on my end, during which I will continue to provide ongoing partial results. I will get back in touch with more questions as I dive deeper later. Best, Yu

…

On Thu, Aug 19, 2021 at 3:38 PM Gregory Way ***@***.***> wrote: cc @ayberman <https://github.com/ayberman> @mekelley <https://github.com/mekelley> I chatted with @yhan8 <https://github.com/yhan8> yesterday, and she is eager to get started! I let her know that September is a good month for the two of you to dedicate to writing the paper. We walked through generating the new batch profiles (now added in #109 <#109>) and I've completed QC (added in #106 <#106> ). @yhan8 <https://github.com/yhan8> approach will be to reproduce the existing analyses by: 1. Creating the conda environment as specified in environment.yml 2. Rerunning the signature generation, evaluation, and visualization in all notebooks provided in the 3.resistance-signature/ folder 3. Tackling these questions above I suspect that September is going to be quite difficult to complete these three analyses as specified above, especially while trying to get up to speed in a completely new data type. @yhan8 <https://github.com/yhan8>, please let us know if you have any questions or concerns, as you make progress towards this goal! Megan and Adi, I think it will also be wise to think a bit about how to use the September writing block if Yu is able to partially answer the three remaining analyses (not complete). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#112 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AR3YBDMCE5XGZ4LAZQTSWDDT5VMSXANCNFSM5CO34QVA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .