= Attendees =

Piet, Tom Goddard, Scooter, Greg, Eric, Elaine

August 1, 2024

= Agenda =

* Selina work in progress

= Discussion Notes =

* Sequence databases
  - Scooter accidentally deleted BLAST and AlphaFold and ESMFold k-mer sequence databases.
  - Databases are not backed up and need to be rebuilt.
  - Cron update scripts rebuilt PDB and NR databases.
  - Tom restored AlphaFold and ESMFold databases.
  - Scooter writing a script to update Uniref databases which were 10 years out of date.

* Selina work in progress
  - Working on CLIP organ segmentation method.
  - Tested on UCSF PHI data, 72 data sets, only 35 usable.
  - Also tried unreleased newer nnUnet organ segmentation from John's Hopkins.  Works slightly better than CLIP.
  - Analyzed different kinds of errors: under segmentation, over segmentation, mixing organs.
  - Ground truth established by eye.  Selina says boundaries are visually clear.
  - Selina made prototype web-site showing results.
  - Scooter suggests next goal is write short paper showing CLIP and nnUnet analysis results.
  - Also want to make a ChimeraX bundle to call a web service to run CLIP or nnUnet.

* Ion classification
  - Responding to manuscript reviewers of MIC paper at Nature Communications.
  - Reviewers wanted a "no ion" class.
  - Working on making an "open bubble" Python module to calculate molecular neighborhood fingerprinting used by MIC.
  - Have made a ChimeraX tool to run it.
  - Will run MIC from ChimeraX on local computer using PyTorch since CPU speed is adequate.

= Action Items =